Electronic structure, bonding, spectroscopy and energetics of Fe-dependent nitrile hydratase active-site models

Fe-type nitrile hydratase (NHase) is a non-heme Fe(III)-dependent enzyme that catalyzes the hydration of nitriles to the corresponding amides. Despite experimental studies of the enzyme and model Fe(III)-containing complexes, many questions concerning the electronic structure and spectroscopic transitions of the metal center remain unanswered. In addition, the catalytic mechanism of nitrile hydration has not yet been determined. We now report density functional theory (B3LYP/6-31G) calculations on three models of the Fe(III) center in the active site of NHase corresponding to hypothetical intermediates in the enzyme-catalyzed hydration of acetonitrile. Together with natural bond orbital (NBO) analysis of the chemical bonding in these active-site models and INDO/S CIS calculations of their electronic spectra, this theoretical investigation gives new insight into the molecular origin of the unusual low-spin preference and spectroscopic properties of the Fe(III) center. In addition, the low-energy electronic transition observed for the active form of NHase is assigned to a dd transition that is coupled with charge-transfer transitions involving the metal and its sulfur ligands. Calculations of isodesmic ligand-exchange reaction energies provide support for coordination of the Fe(III) center in free NHase by a water molecule rather than a hydroxide ion and suggest that the activation of the nitrile substrate by binding to the metal in the sixth coordination site during catalytic turnover cannot yet be definitively ruled out.     

Theoretical investigations of the electronic structure and spectroscopy of mononuclear, non-heme [Fe-NO](6) complexes

The unusual metal coordination and spin-state of the Fe(III) center in nitrile hydratase (NHase) has stimulated the synthesis of numerous model complexes in efforts to understand the reactivity and spectroscopic properties of the enzyme. A particular problem has been the development of model Fe(III) complexes that exhibit reversible, photolabile binding to nitric oxide (NO) in a manner similar to that observed for the NHase metal center. We now report a detailed NBO analysis of the ground-state chemical bonding in three [Fe-NO](6) complexes that exhibit different responses to irradiation, together with investigations of their spectroscopic properties using semiempirical INDO/S CI singles calculations. Our computational studies reveal a correlation between the photolability of these complexes and the existence of low-energy transitions that promote an electron into the Fe-NO pi(*) antibonding molecular orbital. In addition to providing detailed insights into how the ligand field influences the spectroscopy of these mononuclear complexes, these studies strengthen our previous conclusions regarding the role of post-translational cysteine modification in modulating the photoreactivity of the inactive, NO complex of NHase.     

Properties of square-pyramidal alkyl-thiolate Fe(III) complexes, including an analogue of the unmodified form of nitrile hydratase

The syntheses and structures of three new coordinatively unsaturated, monomeric, square-pyramidal thiolate-ligated Fe(III) complexes are described, [Fe(III)((tame-N(3))S(2)(Me2))](+) (1), [Fe(III)(Et-N(2)S(2)(Me2))(py)](1-) (3), and [Fe(III)((tame-N(2)S)S(2)(Me2))](2-) (15). The anionic bis-carboxamide, tris-thiolate N(2)S(3) coordination sphere of 15 is potentially similar to that of the yet-to-be characterized unmodified form of NHase. Comparison of the magnetic and reactivity properties of these reveals how anionic charge build up (from cationic 1 to anionic 3 and dianionic 15) and spin-state influence apical ligand affinity. For all of the ligand-field combinations examined, an intermediate S = 3/2 spin state was shown to be favored by a strong N(2)S(2) basal plane ligand field, and this was found to reduce the affinity for apical ligands, even when they are built in. This is in contrast to the post-translationally modified NHase active site, which is low spin and displays a higher affinity for apical ligands. Cationic 1 and its reduced Fe(II) precursor are shown to bind NO and CO, respectively, to afford [Fe(III)((tame-N(3))S(2)(Me))(NO)](+) (18, nu(NuO) = 1865 cm(-1)), an analogue of NO-inactivated NHase, and [Fe(II)((tame-N(3))S(2)(Me))(CO)] (16; nu(CO) stretch (1895 cm(-1)). Anions (N(3)(-), CN(-)) are shown to be unreactive toward 1, 3, and 15 and neutral ligands unreactive toward 3 and 15, even when present in 100-fold excess and at low temperatures. The curtailed reactivity of 15, an analogue of the unmodified form of NHase, and its apical-oxygenated S = 3/2 derivative [Fe(III)((tame-N(2)SO(2))S(2)(Me2))](2-) (20) suggests that regioselective post-translational oxygenation of the basal plane NHase cysteinate sulfurs plays an important role in promoting substrate binding. This is supported by previously reported theoretical (DFT) calculations.     

Sulfur K-edge XAS and DFT calculations on nitrile hydratase: geometric and electronic structure of the non-heme iron active site

The geometric and electronic structure of the active site of the non-heme iron enzyme nitrile hydratase (NHase) is studied using sulfur K-edge XAS and DFT calculations. Using thiolate (RS(-))-, sulfenate (RSO(-))-, and sulfinate (RSO(2)(-))-ligated model complexes to provide benchmark spectral parameters, the results show that the S K-edge XAS is sensitive to the oxidation state of S-containing ligands and that the spectrum of the RSO(-) species changes upon protonation as the S-O bond is elongated (by approximately 0.1 A). These signature features are used to identify the three cysteine residues coordinated to the low-spin Fe(III) in the active site of NHase as CysS(-), CysSOH, and CysSO(2)(-) both in the NO-bound inactive form and in the photolyzed active form. These results are correlated to geometry-optimized DFT calculations. The pre-edge region of the X-ray absorption spectrum is sensitive to the Z(eff) of the Fe and reveals that the Fe in [FeNO](6) NHase species has a Z(eff) very similar to that of its photolyzed Fe(III) counterpart. DFT calculations reveal that this results from the strong pi back-bonding into the pi antibonding orbital of NO, which shifts significant charge from the formally t(2)(6) low-spin metal to the coordinated NO.     

The role of post-translational modification in the photoregulation of Fe-type nitrile hydratase

The inactive, nitrosyl bound form of Fe-type nitrile hydratase (NHase) contains two active site cysteine residues that are post-translationally modified to sulfenate (SO-) and sulfinate (SO2-) ligands. DFT and INDO/S calculations support the hypothesis that these unusual modifications play a key role in modulating the electronic absorption spectra and photoreactivity of the Fe(III) centre in the enzyme.     

Theoretical investigation of the first-shell mechanism of nitrile hydratase

The first-shell mechanism of nitrile hydratase (NHase) is investigated theoretically using density functional theory. NHases catalyze the conversion of nitriles to amides and are classified into two groups, the non-heme Fe(III) NHases and the non-corrinoid Co(III) NHases. The active site of the non-heme iron NHase comprises a low-spin iron (S=1/2) with a remarkable set of ligands, including two deprotonated backbone nitrogens and both cysteine-sulfenic and cysteine-sulfinic acids. A widely proposed reaction mechanism of NHase is the first-shell mechanism in which the nitrile substrate binds directly to the low-spin iron in the sixth coordination site. We have used quantum chemical models of the NHase active site to investigate this mechanism. We present potential energy profiles for the reaction and provide characterization of the intermediates and transition-state structures for the NHase-mediated conversion of acetonitrile. The results indicate that the first-shell ligand Cys114-SO- could be a possible base in the nitrile hydration mechanism, abstracting a proton from the nucleophilic water molecule. The generally suggested role of the Fe(III) center as a Lewis acid, activating the substrate toward nucleophilic attack, is shown to be unlikely. Instead, the metal is suggested to provide electrostatic stabilization to the anionic imidate intermediate, thereby lowering the reaction barrier.     

Electronic structure of six-coordinate iron(III) monoazaporphyrins

The electronic structures of six-coordinate iron(III) octaethylmonoazaporphyrins, [Fe(MAzP)L 2] (+/-) ( 1), have been examined by means of (1)H NMR and EPR spectroscopy to reveal the effect of meso-nitrogen in the porphyrin ring. The complexes carrying axial ligands with strong field strengths such as 1-MeIm, DMAP, CN (-), and (t)BuNC adopt the low-spin state with the (d xy ) (2)(d xz , d yz ) (3) ground state in a wide temperature range where the (1)H NMR and EPR spectra are taken. In contrast, the complexes with much weaker axial ligands, such as 4-CNPy and 3,5-Cl 2Py, exhibit the spin transition from the mainly S = 3/2 at 298 K to the S = 1/2 with the (d xy ) (2)(d xz , d yz ) (3) ground state at 4 K. Only the THF complex has maintained the S = 3/2 throughout the temperature range examined. Thus, the electronic structures of 1 resemble those of the corresponding iron(III) octaethylporphyrins, [Fe(OEP)L 2] (+/-) ( 2). A couple of differences have been observed, however, in the electronic structures of 1 and 2. One of the differences is the electronic ground state in low-spin bis( (t)BuNC) complexes. While [Fe(OEP)( (t)BuNC) 2] (+) adopts the (d xz , d yz ) (4)(d xy ) (1) ground state, like most of the bis( (t)BuNC) complexes reported previously, [Fe(MAzP)( (t)BuNC) 2] (+) has shown the (d xy ) (2)(d xz , d yz ) (3) ground state. Another difference is the spin state of the bis(3,5-Cl 2Py) complexes. While [Fe(OEP)(3,5-Cl 2Py) 2] (+) has maintained the mixed S = 3/2 and 5/2 spin state from 298 to 4 K, [Fe(MAzP)(3,5-Cl 2Py) 2] (+) has shown the spin transition mentioned above. These differences have been ascribed to the narrower N4 cavity and the presence of lower-lying pi* orbital in MAzP as compared with OEP.     

Spin-State Variations of Iron(III) Complexes with Tetracarbene Macrocycles

Starting from their six-coordinate iron(II) precursor complexes [L^8RFe(MeCN)]²⁺, a series of iron(III) complexes of the known macrocyclic tetracarbene ligand L^8H and its new octamethylated derivative L^8Me, both providing four imidazol-2-yliden donors, were synthesized. Several five- and six-coordinate iron(III) complexes with different axial ligands (Cl⁻, OTf⁻, MeCN) were structurally characterized by X-ray diffraction and analyzed in detail with respect to their spin state variations, using a bouquet of spectroscopic methods (NMR, UV/Vis, EPR, and ⁵⁷Fe Mößbauer). Depending on the axial ligands, either low-spin (S=1/2) or intermediate-spin (S=3/2) states were observed, whereas high-spin (S=5/2) states were inaccessible because of the extremely strong in-plane σ-donor character of the macrocyclic tetracarbene ligands. These findings are reminiscent of the spin state patterns of topologically related ferric porphyrin complexes. The ring conformations and dynamics of the macrocyclic tetracarbene ligands in their iron(II), iron(III) and μ-oxo diiron(III) complexes were also studied.     

The performance of nonhybrid density functionals for calculating the structures and spin states of Fe(II) and Fe(III) complexes

The local density approximation and a range of nonhybrid gradient corrected density functionals (PW91, BLYP, PBE, revPBE, RPBE) have been assessed with respect to the prediction of geometries and spin-state energy preferences for a range of homoleptic Fe(II)L6 and Fe(III)L6 complexes, where L = Cl-, CN-, NH3, pyridine, imidazole, H2O, O=CH2 and tetrahydrofuran. While the qualitative spin-state energies from in vacuo structure optimizations are reasonable the geometries are relatively poorly treated, especially for [FeCl6]3-/4-. Structural results for all the complexes are significantly improved by including environmental effects. The best compromise between structural and spin-state predictive accuracy was obtained for the RPBE functional in combination with the COSMO solvation approach. This approach systematically overestimates the energetic preference for a low spin state, which is partly due to the well-known effect of the lack of exact exchange in nonhybrid functionals and partly due to the larger solvation stabilization of low-spin complexes that have shorter bond lengths and thus smaller molecular volumes than their high-spin partners. Calculations on low spin [Fe(bipy)3]2+ and [Fe(phen)3]2+ and their ortho methyl substituted analogs, which are high spin at room temperature but cross over to low spin at low temperature, suggest the RPBE/COSMO combination generates low spin states which are too stable by approximately 13 kcal mol(-1).     

Neutral bis(alpha-iminopyridine)metal complexes of the first-row transition ions (Cr, Mn, Fe, Co, Ni, Zn) and their monocationic analogues: mixed valency involving a redox noninnocent ligand system

A series of bis(alpha-iminopyridine)metal complexes featuring the first-row transition ions (Cr, Mn, Fe, Co, Ni, and Zn) is presented. It is shown that these ligands are redox noninnocent and their paramagnetic pi radical monoanionic forms can exist in coordination complexes. Based on spectroscopic and structural characterizations, the neutral complexes are best described as possessing a divalent metal center and two monoanionic pi radicals of the alpha-iminopyridine. The neutral M(L*)2 compounds undergo ligand-centered, one-electron oxidations generating a second series, [(L(x))2M(THF)][B(ArF)4] [where L(x) represents either the neutral alpha-iminopyridine (L)0 and/or its reduced pi radical anion (L*)-]. The cationic series comprise mostly mixed-valent complexes, wherein the two ligands have formally different redox states, (L)0 and (L*)-, and the two ligands may be electronically linked by the bridging metal atom. Experimentally, the cationic Fe and Co complexes exhibit Robin-Day Class III behavior (fully delocalized), whereas the cationic Zn, Cr, and Mn complexes belong to Class I (localized) as shown by X-ray crystallography and UV-vis spectroscopy. The delocalization versus localization of the ligand radical is determined only by the nature of the metal linker. The cationic nickel complex is exceptional in this series in that it does not exhibit any ligand mixed valency. Instead, its electronic structure is consistent with two neutral ligands (L)0 and a monovalent metal center or [(L)2Ni(THF)][B(ArF)4]. Finally, an unusual spin equilibrium for Fe(II), between high spin and intermediate spin (S(Fe) = 2 <--> S(Fe) = 1), is described for the complex [(L*)(L)Fe(THF)][B(ArF)4], which consequently is characterized by the overall spin equilibrium (S(tot) = 3/2 <--> S(tot) = 1/2). The two different spin states for Fe(II) have been characterized using variable temperature X-ray crystallography, EPR spectroscopy, zero-field and applied-field M?ssbauer spectroscopy, and magnetic susceptibility measurements. Complementary DFT studies of all the complexes have been performed, and the calculations support the proposed electronic structures.     

Axial ligand and spin-state influence on the formation and reactivity of hydroperoxo-iron(III) porphyrin complexes

The present study focuses on the formation and reactivity of hydroperoxo-iron(III) porphyrin complexes formed in the [Fe(III)(tpfpp)X]/H(2)O(2)/HOO(-) system (TPFPP=5,10,15,20-tetrakis(pentafluorophenyl)-21H,23H-porphyrin; X=Cl(-) or CF(3) SO(3)(-)) in acetonitrile under basic conditions at -15 °C. Depending on the selected reaction conditions and the active form of the catalyst, the formation of high-spin [Fe(III)(tpfpp)(OOH)] and low-spin [Fe(III)(tpfpp)(OH)(OOH)] could be observed with the application of a low-temperature rapid-scan UV/Vis spectroscopic technique. Axial ligation and the spin state of the iron(III) center control the mode of O-O bond cleavage in the corresponding hydroperoxo porphyrin species. A mechanistic changeover from homo- to heterolytic O-O bond cleavage is observed for high- [Fe(III)(tpfpp)(OOH)] and low-spin [Fe(III)(tpfpp)(OH)(OOH)] complexes, respectively. In contrast to other iron(III) hydroperoxo complexes with electron-rich porphyrin ligands, electron-deficient [Fe(III)(tpfpp)(OH)(OOH)] was stable under relatively mild conditions and could therefore be investigated directly in the oxygenation reactions of selected organic substrates. The very low reactivity of [Fe(III)(tpfpp)(OH)(OOH)] towards organic substrates implied that the ferric hydroperoxo intermediate must be a very sluggish oxidant compared with the iron(IV)-oxo porphyrin π-cation radical intermediate in the catalytic oxygenation reactions of cytochrome P450.     

Electronic structure of six-coordinate iron(III)-porphyrin NO adducts: the elusive iron(III)-NO(radical) state and its influence on the properties of these complexes

This paper investigates the interaction between five-coordinate ferric hemes with bound axial imidazole ligands and nitric oxide (NO). The corresponding model complex, [Fe(TPP)(MI)(NO)](BF4) (MI = 1-methylimidazole), is studied using vibrational spectroscopy coupled to normal coordinate analysis and density functional theory (DFT) calculations. In particular, nuclear resonance vibrational spectroscopy is used to identify the Fe-N(O) stretching vibration. The results reveal the usual Fe(II)-NO(+) ground state for this complex, which is characterized by strong Fe-NO and N-O bonds, with Fe-NO and N-O force constants of 3.92 and 15.18 mdyn/A, respectively. This is related to two strong pi back-bonds between Fe(II) and NO(+). The alternative ground state, low-spin Fe(III)-NO(radical) (S = 0), is then investigated. DFT calculations show that this state exists as a stable minimum at a surprisingly low energy of only approximately 1-3 kcal/mol above the Fe(II)-NO(+) ground state. In addition, the Fe(II)-NO(+) potential energy surface (PES) crosses the low-spin Fe(III)-NO(radical) energy surface at a very small elongation (only 0.05-0.1 A) of the Fe-NO bond from the equilibrium distance. This implies that ferric heme nitrosyls with the latter ground state might exist, particularly with axial thiolate (cysteinate) coordination as observed in P450-type enzymes. Importantly, the low-spin Fe(III)-NO(radical) state has very different properties than the Fe(II)-NO(+) state. Specifically, the Fe-NO and N-O bonds are distinctively weaker, showing Fe-NO and N-O force constants of only 2.26 and 13.72 mdyn/A, respectively. The PES calculations further reveal that the thermodynamic weakness of the Fe-NO bond in ferric heme nitrosyls is an intrinsic feature that relates to the properties of the high-spin Fe(III)-NO(radical) (S = 2) state that appears at low energy and is dissociative with respect to the Fe-NO bond. Altogether, release of NO from a six-coordinate ferric heme nitrosyl requires the system to pass through at least three different electronic states, a process that is remarkably complex and also unprecedented for transition-metal nitrosyls. These findings have implications not only for heme nitrosyls but also for group-8 transition-metal(III) nitrosyls in general.     

Electron distribution in iron octaethyloxophlorin complexes. Importance of the Fe(III) oxophlorin trianion form in the bis-pyridine and bis-imidazole complexes

The apportionment of electrons between iron and the porphyrinic macrocycle in complexes of octaethyloxophlorin (H3OEPO) has been a vexing problem. In particular, for (Py)2Fe(OEPO), which is an important intermediate in heme degradation, three resonance structures involving Fe(III), Fe(II), or Fe(I), respectively, have been considered. To clarify this matter, the electronic and geometric structures of (Py)2Fe(III)(OEPO), (Im)2Fe(III)(OEPO).2THF, and (Im)2Fe(III)(OEPO).1.6CHCl3 have been examined by single-crystal X-ray diffraction, measurement of magnetic moments as a function of temperature, and EPR and NMR spectral studies. The results clearly show that both complexes exist in the Fe(III)/oxophlorin trianion form rather than the Fe(II)/oxophlorin radical form previously established for (2,6-xylylNC)(2)Fe(II)(OEPO.). In the solid state from 10 to 300 K, (Py)2Fe(III)(OEPO) exists in the high-spin (S = 5/2) state with the axial ligands in parallel planes, a planar porphyrin, and long axial Fe-N distances. However, in solution it exists predominantly in a low-spin (S = 1/2) form. In contrast, the structures of (Im)2Fe(III)(OEPO).2THF and (Im)2Fe(III)(OEPO).1.6CHCl3 consist of porphyrins with a severe ruffled distortion, axial ligands in nearly perpendicular planes, and relatively short axial Fe-N distances. The crystallographic, magnetic, EPR, and NMR results all indicate that (Im)2Fe(III)(OEPO) exists in the low-spin Fe(III) form in both the solid state and in solution.     

Correlation of spin states and spin delocalization with the dioxygen reactivity of catecholatoiron(III) complexes

A series of catecholatoiron(III) complexes, [Fe(III)L(4Cl-cat)]BPh4 (L = (4-MeO)2TPA (1), TPA (2), (4-Cl)2TPA (3), (4-NO2)TPA (4), (4-NO2)2TPA (5); TPA = tris(pyridin-2-ylmethyl)amine; 4Cl-cat = 4-chlorocatecholate), have been characterized by magnetic susceptibility measurements and EPR, 1H NMR, and UV-vis-NIR spectroscopies to clarify the correlation of the spin delocalization on the catecholate ligand with the O2 reactivity as well as the spin-state dependence of the O2 reactivity. EPR spectra in frozen CH3CN at 123 K clearly showed that introduction of electron-withdrawing groups effectively shifts the spin equilibrium from a high-spin to a low-spin state. The effective magnetic moments determined by the Evans method in a CH3CN solution showed that 5 contains 36% of low-spin species at 243 K, while 1-4 are predominantly in a high-spin state. Evaluation of spin delocalization on the 4Cl-cat ligand by paramagnetic 1H NMR shifts revealed that the semiquinonatoiron(II) character is more significant in the low-spin species than in the high-spin species. The logarithm of the reaction rate constant is linearly correlated with the energy gap between the catecholatoiron(III) and semiquinonatoiron(II) states for the high-spin complexes 1-3, although complexes 4 and 5 deviate negatively from linearity. The lower reactivity of the low-spin complex, despite its higher spin density on the catecholate ligand compared with the high-spin analogues, suggests the involvement of the iron(III) center, rather than the catecholate ligand, in the reaction with O2.     

On the structure and spin states of Fe(III)-EDDHA complexes

DFT methods are suitable for predicting both the geometries and spin states of EDDHA-Fe(III) complexes. Thus, extensive DFT computational studies have shown that the racemic-Fe(III) EDDHA complex is more stable than the meso isomer, regardless of the spin state of the central iron atom. A comparison of the energy values obtained for the complexes under study has also shown that high-spin (S = 5/2) complexes are more stable than low-spin (S = 1/2) ones. These computational results matched the experimental results of the magnetic susceptibility values of both isomers. In both cases, their behavior has been fitted as being due to isolated high-spin Fe(III) in a distorted octahedral environment. The study of the correlation diagram also confirms the high-spin iron in complex 2b. The geometry optimization of these complexes performed with the standard 3-21G* basis set for hydrogen, carbon, oxygen, and nitrogen and the Hay-Wadt small-core effective core potential (ECP) including a double-xi valence basis set for iron, followed by single-point energy refinement with the 6-31G* basis set, is suitable for predicting both the geometries and the spin-states of EDDHA-Fe(III) complexes. The presence of a high-spin iron in Fe(III)-EDDHA complexes could be the key to understanding their lack of reactivity in electron-transfer processes, either chemically or electrochemically induced, and their resistance to photodegradation.