Radical S-Adenosyl-l-Methionine Enzyme PylB: A C-Centered Radical to Convert l-Lysine into (3R)-3-Methyl-d-Ornithine

PylB is a radical S-adenosyl-l-methionine (SAM) enzyme predicted to convert l-lysine into (3R)-3-methyl-d-ornithine, a precursor in the biosynthesis of the 22nd proteogenic amino acid pyrrolysine. This protein highly resembles that of the radical SAM tyrosine and tryptophan lyases, which activate their substrate by abstracting a H atom from the amino-nitrogen position. Here, combining in vitro assays, analytical methods, electron paramagnetic resonance spectroscopy, and theoretical methods, we demonstrated that instead, PylB activates its substrate by abstracting a H atom from the Cγ position of l-lysine to afford the radical-based β-scission. Strikingly, we also showed that PylB catalyzes the reverse reaction, converting (3R)-3-methyl-d-ornithine into l-lysine and using catalytic amounts of the 5'-deoxyadenosyl radical. Finally, we identified significant in vitro production of 5'-thioadenosine, an unexpected shunt product that we propose to result from the quenching of the 5'-deoxyadenosyl radical species by the nearby [Fe4S4] cluster.

Hybrid CdSe/ZnS Quantum Dot-Gold Nanoparticle Composites Assembled by Click Chemistry: Toward Affordable and Efficient Redox Photocatalysts Working with Visible Light

A new modular, easy-to-synthesize photocatalyst was prepared by assembling colloidal CdSe/ZnS quantum dots (QD) and gold nanoparticles (AuNP) via their ligands thanks to copper-catalyzed azide to alkyne cycloaddition (CuAAC) click chemistry. The resulting composite (QD-AuNP) photocatalyst was tested with a benchmark photoredox system previously reported by our group, for which QD alone acted as a photocatalyst but with a modest quantum yield (QY = 0.06%) and turnover number (TON = 350 in 3 h) due to poor charge separation. After optimization, the QD-AuNP composites exhibited much improved photocatalytic performances: up to five times higher TON (2600 in 3 h) and up to 24 times faster reaction in the first 10 min of visible irradiation. Such an improvement is attributed to an efficient electron transfer from QD to AuNP in the photoexcited QD-AuNP composites, which ensures a much better charge separation than that in QD alone. This was confirmed by studying both (i) the quenching of the QD photoluminescence during the synthesis of the QD-AuNP composites and (ii) the blue shift of the AuNP plasmon absorption band due to the accumulation of up to 7400 electrons per AuNP in QD-AuNP composites under visible light irradiation in the presence of electron donors.

Partial Deoxygenative CO Homocoupling by a Diiron Complex

One route to address climate change is converting carbon dioxide to synthetic carbon-neutral fuels. Whereas carbon dioxide to CO conversion has precedent in homo- and heterogeneous catalysis, deoxygenative coupling of CO to products with C-C bonds-as in liquid fuels-remains challenging. Here, we report coupling of two CO molecules by a diiron complex. Reduction of Fe2 (CO)2 L (2), where L2- is a bis(β-diketiminate) cyclophane, gives [K(THF)5 ][Fe2 (CO)2 L] (3), which undergoes silylation to Fe2 (CO)(COSiMe3 )L (4). Subsequent C-OSiMe3 bond cleavage and C=C bond formation occurs upon reduction of 4, yielding Fe2 (μ-CCO)L. CO derived ligands in this series mediate weak exchange interactions with the ketenylidene affording the smallest J value, with changes to local metal ion spin states and coupling schemes (ferro- vs. antiferromagnetism) based on DFT calculations, Mössbauer and EPR spectroscopy. Finally, reaction of 5 with KEt3 BH or methanol releases the C2 O2- ligand with retention of the diiron core.

Fine Tuning of Quantum Dots Photocatalysts for the Synthesis of Tropane Alkaloid Skeletons

Several types of Quantum Dots (QDs) (CdS, CdSe and InP, as well as core-shell QDs such as type I InPZnS, quasi type-II CdSe-CdS and inverse type-I CdS-CdSe) were considered for generating α-aminoalkyl free radicals. The feasibility of the oxidation of the N-aryl amines and the generation of the desired radical was evidenced experimentally by quenching of the photoluminescence of the QDs and by testing a vinylation reaction using an alkenylsulfone radical trap. The QDs were tested in a radical [3+3]annulation reaction giving access to tropane skeletons and that requires the completion of two consecutive catalytic cycles. Several QDs such as CdS core, CdSe core and inverted type I CdS-CdSe core-shell proved to be efficient photocatalysts for this reaction. Interestingly, the addition of a second shorter chain ligand to the QDs appeared to be essential to complete the second catalytic cycle and to obtain the desired bicyclic tropane derivatives. Finally, the scope of the [3+3]-annulation reaction was explored for the best performing QDs and isolated yields that compares well with classical iridium photocatalysis were obtained.

Redox-Switchable Behavior of Transition-Metal Complexes Supported by Amino-Decorated N-Heterocyclic Carbenes

The coordination chemistry of the N-heterocyclic carbene ligand IMes^(NMe2)2, derived from the well-known IMes ligand by substitution of the carbenic heterocycle with two dimethylamino groups, was investigated with d⁶ [Mn(I), Fe(II)], d⁸ [Rh(I)], and d¹⁰ [Cu(I)] transition-metal centers. The redox behavior of the resulting organometallic complexes was studied through a combined experimental/theoretical study, involving electrochemistry, EPR spectroscopy, and DFT calculations. While the complexes [CuCl(IMes^(NMe2)2)], [RhCl(COD)(IMes^(NMe2)2)], and [FeCp(CO)₂ (IMes^(NMe2)2)](BF₄) exhibit two oxidation waves, the first oxidation wave is fully reversible but only for the first complex the second oxidation wave is reversible. The mono-oxidation event for these complexes occurs on the NHC ligand, with a spin density mainly located on the diaminoethylene NHC-backbone, and has a dramatic effect on the donating properties of the NHC ligand. Conversely, as the Mn(I) center in the complex [MnCp(CO)₂ ((IMes^(NMe2)2)] is easily oxidizable, the latter complex is first oxidized on the metal center to form the corresponding cationic Mn(II) complex, and the NHC ligand is oxidized in a second reversible oxidation wave.

Electrocatalytic reduction of protons to dihydrogen by the cobalt tetraazamacrocyclic complex [Co(N4H)Cl2]+: mechanism and benchmarking of performances

The cobalt tetraazamacrocyclic [Co(N₄H)Cl₂]⁺ complex is becoming a popular and versatile catalyst for the electrocatalytic evolution of hydrogen, because of its stability and superior activity in aqueous conditions. We present here a benchmarking of its performances based on the thorough analysis of cyclic voltammograms recorded under various catalytic regimes in non-aqueous conditions allowing control of the proton concentration. This allowed a detailed mechanism to be proposed with quantitative determination of the rate-constants for the various protonation steps, as well as identification of the amine function of the tetraazamacrocyclic ligand to act as a proton relay during H₂ evolution.

Half-sandwich manganese complexes Cp(CO)2Mn(NHC) as redox-active organometallic fragments

Oxidation of the half-sandwich Mn^I complexes Cp(CO)₂Mn(NHC) bearing dialkyl-, arylalkyl- and diarylsubstituted N-heterocyclic carbene ligands (NHC = IMe, IMeMes, IMes) affords the corresponding stable Mn^II radical cations [Cp(CO)₂Mn(NHC)](BF₄) isolated in 92-95% yield. Systematic X-ray diffraction studies of the series of Mn^I and Mn^II NHC complexes revealed the expected characteristic structural changes upon oxidation, namely the elongation of the Mn-CO and Mn-NHC bonds as well as the diminution of the OC-Mn-CO angle. ESR spectra of [Cp(CO)₂Mn(IMes)](BF₄) in frozen solution (CH₂Cl₂/toluene 1 : 1, 70 K) allowed the identification of two conformers for this complex and their structural assignment using DFT calculations. The stability of these NHC complexes in both metal oxidation states, moderate oxidation potentials and the ease of detection of Mn^II species by a variety of spectroscopic techniques (UV-Vis, IR, paramagnetic ¹H NMR, and ESR) make these compounds promising objects for applications as redox-active organometallic fragments.

Electron and Proton Transfers Modulate DNA Binding by the Transcription Regulator RsrR

The [Fe₂S₂]-RsrR gene transcription regulator senses the redox status in bacteria by modulating DNA binding, while its cluster cycles between +1 and +2 states-only the latter binds DNA. We have previously shown that RsrR can undergo remarkable conformational changes involving a 100° rotation of tryptophan 9 between exposed (Out) and buried (In) states. Here, we have used the chemical modification of Trp9, site-directed mutagenesis, and crystallographic and computational chemical studies to show that (i) the Out and In states correspond to oxidized and reduced RsrR, respectively, (ii) His33 is protonated in the In state due to a change in its pK_a caused by cluster reduction, and (iii) Trp9 rotation is conditioned by the response of its dipole moment to environmental electrostatic changes. Our findings illustrate a novel function of protonation resulting from electron transfer.

Immobilization of Mn(i) and Ru(ii) polypyridyl complexes on TiO2 nanoparticles for selective photoreduction of CO2 to formic acid

Under visible irradiation in DMF/TEOA, the hybrid nanomaterial Ru(ii)/TiO₂/Mn(i), lead to the selective reduction of CO₂ into HCOO⁻.

[Cr(ttpy)2]3+ as a multi-electron reservoir for photoinduced charge accumulation

[Cr(ttpy)2]3+ (ttpy = 4'-(4-methylphenyl)-2,2':6,2''-terpyridine) exhibits rich electrochemical and photophysical properties. Cyclic voltammetry performed in CH3CN shows in the cathodic part the presence of three one-electron reversible systems at -0.47, -0.85 and -1.35 V vs. Ag/AgNO3 10-2 M. These systems are attributed to the reduction of the terpyridine ligands with a partial delocalization of the charge on the tolyl for the last reduction event. The three different reduced species were generated by exhaustive electrolysis and characterized by EPR and UV-visible spectroscopy; DFT calculations were performed to locate the spin density of the electrons added during the reduction. Visible light irradiation of [Cr(ttpy)2]3+ induces the population of a luminescent metal-centered excited state with a lifetime of 270 ns in deoxygenated CH3CN. This excited state can be quenched by an electron transfer process with triphenylphosphine (PPh3) or triethanolamine (TEOA). Using TEOA as a sacrificial electron donor, the doubly reduced species (i.e.[Cr(ttpy)2] +) can be generated under continuous irradiation. In the presence of [Ru(bpy)3]2+ as an additional photosensitizer, the photoreduction of [Cr(ttpy)2]3+ towards [Cr(ttpy)2]+ is accelerated. The trinuclear [{RuII(bpy)2(bpy-O-tpy)}2CrIII]7+ complex ([Ru2Cr]7+) in which a CrIII-bis-terpyridine centre is covalently linked to two RuII-tris-bipyridine moieties by oxo bridges has been synthesised. Its electrochemical, photophysical and photochemical properties were investigated in deoxygenated CH3CN. Cyclic voltammetry indicates only a poor electronic communication between the different subunits, whereas luminescence experiments show a strong quenching of the RuII* excited state by an intramolecular process. Continuous irradiation of [Ru2Cr]7+ under visible conditions in the presence of TEOA leads to [Ru2Cr]4+ where three electrons are stored on the [Cr(ttpy)] subunit.

Radical S-Adenosyl-l-methionine Tryptophan Lyase (NosL): How the Protein Controls the Carboxyl Radical •CO2- Migration

The radical S-adenosyl-l-methionine tryptophan lyase uses radical-based chemistry to convert l-tryptophan into 3-methyl-2-indolic acid, a fragment in the biosynthesis of the thiopeptide antibiotic nosiheptide. This complex reaction involves several successive steps corresponding to (i) the activation by a specific hydrogen-atom abstraction, (ii) an unprecedented •CO₂^- radical migration, (iii) a cyanide fragment release, and (iv) the termination of the radical-based reaction. In vitro study of this reaction is made more difficult because the enzyme produces a significant amount of a shunt product instead of the natural product. Here, using a combination of X-ray crystallography, electron paramagnetic resonance spectroscopy, and quantum and hybrid quantum mechanical/molecular mechanical calculations, we have deciphered the fine mechanism of the key •CO₂^- radical migration, highlighting how the preorganized active site of the protein tightly controls this reaction.

Highly Efficient Tuning of Ferromagnetic Spin Interactions in High-Spin Arylamine Structures by Incorporation of Spin Bearing Carbazole Units

Arylamine moieties oxidized to radical cations are considered promising spin bearing units in high-spin-type compounds. Here, we report the first use of carbazole-3,6-diamine units as efficient, rigid spin containing units. The use of rigid spin bearing units enhances significantly spin exchange interactions. The design using density functional theory calculations shows the progressive increase of the exchange coupling constant dependent on the considered model molecules. Two of the most representative molecules containing flexible (dimer 1) and rigid spin coupling unit (dimer 2) were synthesized. Electrochemical and pulsed-electron paramagnetic resonance nutation studies showed that both dimers can be oxidized to yield a majority of dicationic diradicals exhibiting S = 1 ground states. The high values of the dimer 2 exchange coupling constant obtained both computationally ( J/ k_B = 145 K; H_Heis. = - JS₁ S₂) and experimentally ( J/ k_B = 90-100 K) indicate the beneficial role of the carbazole moiety incorporated into spin bearing units.

Time-gated triplet-state optical spectroscopy to decipher organic luminophores embedded in rigid matrices

Wet-chemically synthesized inorganic materials often exhibit luminescence behavior. We have recently shown that the amorphous yttrium-aluminium-borate (a-YAB) powders obtained by sol-gel and modified Pechini methods exhibit organic impurities, responsible for their intense visible photoluminescence and phosphorescence afterglow. However, the heterogeneity of impurity organic compounds and difficulties in their intact extraction from the solid inorganic host matrix limit the extraction-based chemical analysis for luminophore identification. Here, we propose a photo-physical route based on time-gated triplet-state optical spectroscopy (TGTSS) to construct the electronic structures of the trapped unknown luminophores, which successfully illustrates the luminescence properties of a-YAB powders in more detail and also provides important insights intrinsic to the nature of the luminophores. The experimental results accompanied with TD-DFT calculations of the theoretical electronic structures thus help us to propose the probable luminophore compounds trapped in rigid a-YAB matrices. We anticipate that the present approach will open new opportunities for analyzing similar complex luminescent materials, including carbon dots, graphene oxides, etc., which is vital for their improvement.

X-ray structural, functional and computational studies of the O2-sensitive E. coli hydrogenase-1 C19G variant reveal an unusual [4Fe-4S] cluster

The crystal structure of the Escherichia coli O2-sensitive C19G [NiFe]-hydrogenase-1 variant shows that the mutation results in a novel FeS cluster, proximal to the Ni-Fe active site. While the proximal cluster of the native O2-tolerant enzyme can transfer two electrons to that site, EPR spectroscopy shows that the modified cluster can transfer only one electron, this shortfall coinciding with O2 sensitivity. Computational studies on electron transfer help to explain how the structural and redox properties of the novel FeS cluster modulate the observed phenotype.

An artificial photosynthetic system for photoaccumulation of two electrons on a fused dipyridophenazine (dppz)-pyridoquinolinone ligand

Increasing the efficiency of molecular artificial photosynthetic systems is mandatory for the construction of functional devices for solar fuel production. Decoupling the light-induced charge separation steps from the catalytic process is a promising strategy, which can be achieved thanks to the introduction of suitable electron relay units performing charge accumulation. We report here on a novel ruthenium tris-diimine complex able to temporarily store two electrons on a fused dipyridophenazine-pyridoquinolinone π-extended ligand upon visible-light irradiation in the presence of a sacrificial electron donor. Full characterization of this compound and of its singly and doubly reduced derivatives thanks to resonance Raman, EPR and (TD)DFT studies allowed us to localize the two electron-storage sites and to relate charge photoaccumulation with proton-coupled electron transfer processes.

Unveiling the redox-active character of imidazolin-2-thiones derived from amino-substituted N-heterocyclic carbenes

Spectroscopic, structural and computational studies on the amino-substituted imidazolin-2-thiones reveal the imidazolyl ring to be redox active.

Evidence of Organic Luminescent Centers in Sol-Gel-Synthesized Yttrium Aluminum Borate Matrix Leading to Bright Visible Emission

Yttrium aluminum borate (YAB) powders prepared by sol-gel process have been investigated to understand their photoluminescence (PL) mechanism. The amorphous YAB powders exhibit bright visible PL from blue emission for powders calcined at 450 °C to broad white PL for higher calcination temperature. Thanks to ¹³ C labelling, NMR and EPR studies show that propionic acid initially used to solubilize the yttrium nitrate is decomposed into aromatic molecules confined within the inorganic matrix. DTA-TG-MS analyses show around 2 wt % of carbogenic species. The PL broadening corresponds to the apparition of a new band at 550 nm, associated with the formation of aromatic species. Furthermore, pulsed ENDOR spectroscopy combined with DFT calculations enables us to ascribe EPR spectra to free radicals derived from small (2 to 3 rings) polycyclic aromatic hydrocarbons (PAH). PAH molecules are thus at the origin of the PL as corroborated by slow afterglow decay and thermoluminescence experiments.

Welcoming natural isotopic abundance in solid-state NMR: probing π-stacking and supramolecular structure of organic nanoassemblies using DNP

The low natural abundance of ¹³C combined with MAS-DNP enables ¹³C–¹³C polarization transfer up to ∼7 Å and observation of π-stacking.

The self-assembly of small organic molecules is an intriguing phenomenon, which provides nanoscale structures for applications in numerous fields from medicine to molecular electronics. Detailed knowledge of their structure, in particular on the supramolecular level, is a prerequisite for the rational design of improved self-assembled systems. In this work, we prove the feasibility of a novel concept of NMR-based 3D structure determination of such assemblies in the solid state. The key point of this concept is the deliberate use of samples that contain ¹³C at its natural isotopic abundance (NA, 1.1%), while exploiting magic-angle spinning dynamic nuclear polarization (MAS-DNP) to compensate for the reduced sensitivity. Since dipolar truncation effects are suppressed to a large extent in NA samples, unique and highly informative spectra can be recorded which are impossible to obtain on an isotopically labeled system. On the self-assembled cyclic diphenylalanine peptide, we demonstrate the detection of long-range internuclear distances up to ∼7 Å, allowing us to observe π-stacking through ¹³C–¹³C correlation spectra, providing a powerful tool for the analysis of one of the most important non-covalent interactions. Furthermore, experimental polarization transfer curves are in remarkable agreement with numerical simulations based on the crystallographic structure, and can be fully rationalized as the superposition of intra- and intermolecular contributions. This new approach to NMR crystallography provides access to rich and precise structural information, opening up a new avenue to de novo crystal structure determination by NMR.

Metal sensing and signal transduction by CnrX from Cupriavidus metallidurans CH34: role of the only methionine assessed by a functional, spectroscopic, and theoretical study

When CnrX, the periplasmic sensor protein in the CnrYXH transmembrane signal transduction complex of Cupriavidus metallidurans CH34, binds the cognate metal ions Ni(II) or Co(II), the ECF-type sigma factor CnrH is made available in the cytoplasm for the RNA-polymerase to initiate transcription at the cnrYp and cnrCp promoters. Ni(II) or Co(II) are sensed by a metal-binding site with a N3O2S coordination sphere with octahedral geometry, where S stands for the thioether sulfur of the only methionine (Met123) residue of CnrX. The M123A-CnrX derivative has dramatically reduced signal propagation in response to metal sensing while the X-ray structure of Ni-bound M123A-CnrXs showed that the metal-binding site was not affected by the mutation. Ni(II) remained six-coordinate in M123A-CnrXs, with a water molecule replacing the sulfur as the sixth ligand. H32A-CnrXs, the soluble model of the wild-type membrane-anchored CnrX, was compared to the double mutants H32A-M123A-CnrXs and H32A-M123C-CnrXs to spectroscopically evaluate the role of this unique ligand in the binding site of Ni or Co. The Co- and Ni-bound forms of the protein display unusually blue-shifted visible spectra. TD-DFT calculations using structure-based models allowed identification and assignment of the electronic transitions of Co-bound form of the protein and its M123A derivative. Among them, the signature of the S-Co transition is distinguishable in the shoulder at 530 nm. In vitro affinity measurements point out the crucial role of Met123 in the selectivity for Ni or Co, and in vivo data support the conclusion that Met123 is a trigger of the signal transduction.

Experimental and theoretical study of the n-doped successive polyanions of oligocruciform molecular wires: up to five units of charge

The electronic structure of polyanions of sterically encumbered triisopropylsilyl-substituted linear and cyclic oligo(phenyleneethynylene)s (Monomer, Trimer, Pentamer, and Triangle) is investigated by electron paramagnetic resonance (EPR), electron nuclear double resonance (ENDOR), and UV/Vis-near-infrared (NIR) spectroscopies, cyclic voltammetry, and theoretical calculations (DFT). Increasing anion orders are generated sequentially in vacuo at room temperature by chemical reaction with potassium metal up to the pentaanion. The relevance of these compounds acting as electron reservoirs is thus demonstrated. Even-order anions are EPR silent, whereas the odd species exhibit different signatures, which are identified after comparison of the measured hyperfine couplings by ENDOR spectroscopy with those predicted by DFT calculations. With increasing size of the oligomers the electron spin density is first distributed over the backbone carbon atoms for the monoanions, and then further localized at the outer phenyl rings for the trianion species. Examination of the UV/Vis-NIR spectra indicates that the monoanions (T(.-) , P(.-) ) exhibit two transitions in the Vis-NIR region, whereas a strong absorption in the IR region is solely observed for higher reduced states. Electronic transitions of the neutral monoanions and trianions are redshifted with increasing oligomer size, whereas for a given oligomer a blueshift is observed upon increasing the charge, which suggests a localization of the spin density.

Two Fe-S clusters catalyze sulfur insertion by radical-SAM methylthiotransferases

How living organisms create carbon-sulfur bonds during the biosynthesis of critical sulfur-containing compounds is still poorly understood. The methylthiotransferases MiaB and RimO catalyze sulfur insertion into tRNAs and ribosomal protein S12, respectively. Both belong to a subgroup of radical-S-adenosylmethionine (radical-SAM) enzymes that bear two [4Fe-4S] clusters. One cluster binds S-adenosylmethionine and generates an Ado• radical via a well-established mechanism. However, the precise role of the second cluster is unclear. For some sulfur-inserting radical-SAM enzymes, this cluster has been proposed to act as a sacrificial source of sulfur for the reaction. In this paper, we report parallel enzymological, spectroscopic and crystallographic investigations of RimO and MiaB, which provide what is to our knowledge the first evidence that these enzymes are true catalysts and support a new sulfation mechanism involving activation of an exogenous sulfur cosubstrate at an exchangeable coordination site on the second cluster, which remains intact during the reaction.

Analysis of the singlet-triplet splitting computed by the density functional theory-broken-symmetry method: is it an exchange coupling constant?

We derive an analytical expression of the density functional theory (DFT)-broken-symmetry (BS) estimation J(BS) of the singlet-triplet gap at the "3 sites-4 electrons" level, that is, two S = (1)/(2) metallic sites + one diamagnetic bridge orbital. As originally designed by Noodleman and Davidson (Chem. Phys.1986, 109, 131), J(BS) contains the residual ferromagnetic contribution, single ligand-to-metal and metal-to-metal charge-transfer terms, but no double ligand-to-metal charge-transfer terms or intra/interligand spin-polarization terms. As revealed by the present analysis, the triplet and BS states computed by DFT differ, not only perturbatively (as expected) because of the various physical mechanisms involved (i.e., differential charge-transfer terms) but mainly because of a spurious and unphysical symmetry breaking of the bridge orbitals in the BS state. We examine the consequences of such a difference by deriving two analytical expressions of the exchange coupling constant, one from the BS orbitals designed to match J(BS) and another one from triplet orbitals only. Following and extending on the first paper in the series (J. Phys. Chem. A 2010, 114, 6149), we propose a simple procedure to extract appropriate parameters filling in our analytical expressions. Moreover, we derive the equivalent "3 sites-4 electrons" exchange coupling constant in the configuration-interaction approach, J(CI), for the purpose of comparison. These analytical expressions have been applied to various copper dimers and compared to experimental values.

Carbon monoxide dehydrogenase reaction mechanism: a likely case of abnormal CO2 insertion to a Ni-H(-) bond

Ni-containing carbon monoxide dehydrogenases (CODH), present in many anaerobic microorganisms, catalyze the reversible oxidation of CO to CO(2) at the so-called C-cluster. This atypical active site is composed of a [NiFe(3)S(4)] cluster and a single unusual iron ion called ferrous component II or Fe(u) that is bridged to the cluster via one sulfide ion. After additional refinement of recently published high-resolution structures of COOH(x)-, OH(x)-, and CN-bound CODH from Carboxydothermus hydrogenoformans (Jeoung and Dobbek Science 2007, 318, 1461-1464; J. Am. Chem. Soc. 2009, 131, 9922-9923), we have used computational methods on the predominant resulting structures to investigate the spectroscopically well-characterized catalytic intermediates, C(red1) and the two-electron more-reduced C(red2). Several models were geometry-optimized for both states using hybrid quantum mechanical/molecular mechanical potentials. The comparison of calculated Mössbauer parameters of these active site models with experimental data allows us to propose that the C(red1) state has a Fe(u)-Ni(2+) bridging hydroxide ligand and the C(red2) state has a hydride terminally bound to Ni(2+). Using our combined structural and theoretical data, we put forward a revised version of an earlier proposal for the catalytic cycle of Ni-containing CODH (Volbeda and Fontecilla-Camps Dalton Trans. 2005, 21, 3443-3450) that agrees with available spectroscopic and structural data. This mechanism involves an abnormal CO(2) insertion into the Ni(2+)-H(-) bond.

Valence bond/broken symmetry analysis of the exchange coupling constant in copper(II) dimers. Ferromagnetic contribution exalted through combined ligand topology and (singlet) covalent-ionic mixing

In this paper we aim at presenting a full-VB (valence-bond) analysis of the DFT broken symmetry (BS) exchange coupling constant J(BS). We extend Kahn and Briat's "two sites-two electrons" VB original formalism (Kahn, O.; Briat, B. J. Chem. Soc. Farady Trans. II, 1976, 72, 268) by taking into account the covalent-ionic singlet state mixing, here translated into intersite magnetic orbital delocalization. In this way, two explicit contributions to the magnetic orbital overlap appear, one from the purely covalent state, and the other one from the covalent-ionic mixing. This scheme allows us to relax the strict orthogonality constraint of Kahn and Briat's chemically heuristic model resulting into ferromagnetism. Moreover, we show how DFT-BS calculations applied to various copper(II) dimers yield effective parameters that can be injected into the full-VB model, allowing for a breaking down of J(BS) into various contributions, one of which being either ferromagnetic or antiferromagnetic depending on the bridging ligand topology. Two classes of systems emerge from this analysis and the exceptional ferromagnetic coupling property of the "end-on" azido-bridged copper dimer is especially emphasized.

Verdoheme formation in Proteus mirabilis catalase

BACKGROUND

Heme oxidative degradation has been extensively investigated in peroxidases but not in catalases. The verdoheme formation, a product of heme oxidation which inactivates the enzyme, was studied in Proteus mirabilis catalase.

METHODS

The verdoheme was generated by adding peracetic acid and analyzed by mass spectrometry and spectrophotometry.

RESULTS

Kinetics follow-up of different catalase reactional intermediates shows that i) the formation of compound I always precedes that of verdoheme, ii) compound III is never observed, iii) the rate of compound II decomposition is not compatible with that of verdoheme formation, and iv) dithiothreitol prevents the verdoheme formation but not that of compound II, whereas NADPH prevents both of them. The formation of verdoheme is strongly inhibited by EDTA but not increased by Fe3+ or Cu2+ salts. The generation of verdoheme is facilitated by the presence of protein radicals as observed in the F194Y mutated catalase. The inability of the inactive variant (H54F) to form verdoheme, indicates that the heme oxidation is fully associated to the enzyme catalysis.

CONCLUSION

These data, taken together, strongly suggest that the verdoheme formation pathway originates from compound I rather than from compound II.

GENERAL SIGNIFICANCE

The autocatalytic verdoheme formation is likely to occur in vivo.

Variation of average g values and effective exchange coupling constants among [2Fe-2S] clusters: a density functional theory study of the impact of localization (trapping forces) versus delocalization (double-exchange) as competing factors

A phenomenological model aimed at rationalizing variations in both average g-tensor values (gav identical with 1/3Sigmaigi ) and effective exchange coupling constants Jeff (defined as two-thirds of the energy difference between the S = 3/2 and S = 1/2 spin states) has been derived in order to describe the great variety of magnetic properties exhibited by reduced [2Fe-2S] clusters in proteins. The key quantity in the present analysis is the ratio Delta E/B computed from two competing terms. Delta Ecomprises various effects that result in trapping-site asymmetries: vibronic coupling and the chemical nature (S/N/O) and conformations of the ligands on the one hand and solvation terms, the hydrogen bonding network, etc., on the other. All of these additive terms (in a "bottom-up" approach) favor valence localization of the reducing electron onto one of the two iron sites. In contrast, the B term is the double-exchange term, which favors electronic delocalization. Both gav and Jeff can be expressed as functions of Delta E/ B. We have also shown that electronic localization generally favors small gav and large Jeff values (while the opposite is true for electronic delocalization) in a comparative study of the spectroscopic features of plant-type ferredoxins (Fd's) and Rieske centers (and related mutants). Two other types of problems were particularly challenging. The first of these involved deprotonated Rieske centers and the xanthine oxidase clusters II, which are characterized by very small Jeff values (40-45 cm (-1) with a J S A. S B model) correlated with unusually large gav values (in the range 1.97-2.01) as a result of an antisymmetric exchange coupling mechanism. The second concerned the analogous Fd's from Clostridium pasteurianum (Cp) and Aquifex aeolicus (Aa). Detailed Mössbauer studies of the C56S mutant of the Cp system revealed a mixture of clusters with valence-localized S = 1/2 and valence-delocalized S = 9/2 ground states. We relied on crystallographic structures of wild-type and mutant Aa Fd's in order to explain such a distribution of spin states.

An Unprecedented Asymmetric End-On Azido-Bridged Copper(II) Imino Nitroxide Complex: Structure, Magnetic Properties, and Density Functional Theory Analysis

The dinuclear copper(II) complex [Cu2(mu(1,1)-N3)2(im-2py)2(N3)2] [im-2py = 2-(2-pyridyl)-4,4,5,5-tetramethylimidazolinyl-1-oxy] has been prepared and structurally characterized. The crystal structure consists of a dinuclear unit in which the Cu(II) ions are bridged by two azido ions in a end-on asymmetric fashion and the imino nitroxide radicals are chelating by the two imino N atoms. Accordingly, the magnetic susceptibility data were analyzed considering a linear spin-coupling scheme rad(1)-Cu(2)-Cu(3)-rad(4) (with Si = 1/2, i = 1-4), where the Heisenberg spin Hamiltonian assumes the general form -2Sigma(i)<(j)S(i)S(j). Considering only first-neighbor spin-coupling constants (J13 = J24 = J14 = 0), magnetic susceptibility measurements show that the copper(II) imino nitroxide rad-Cu-(Cu-rad)(rad-Cu)-Cu-rad exchange coupling is ferromagnetic and large (J12 = J34 = J1 > +190 cm(-1)), as is expected for copper imino nitroxide species, and the copper-copper (rad)-Cu-Cu-(rad) coupling through the asymmetric double end-on azide bridges appeared antiferromagnetic and rather large [J23 = J2 = -43(2) cm(-1)]. By contrast, a density functional theory analysis of the system through the computation of broken-symmetry-state energies resulted in J2 approximately 0 cm(-1). This apparent paradox is resolved by introducing a second-neighbor rad-(Cu)-Cu-(rad)(rad)-Cu-(Cu)-rad spin-coupling constant J13 = J24 = J3, which turns out to be antiferromagnetic both experimentally (when J2 is set equal to zero) and computationally.

Study of Photoinduced N-Hydroxy-arylnitroxide Radicals (ArNO•OH) by Time-Resolved EPR

The photoreduction of aromatic nitro compounds by alcohols is a well-known reaction; however, the first stages of its mechanism remain controversial. This study aims at characterizing the "primary" radicalar transients involved in this reaction by EPR spectroscopy. Laser flash photolysis (lambda = 266 nm) of nitrobenzene, 5-nitrouracil, p-nitroacetophenone, o-propylnitrobenzene, and 2-nitroresorcinol in ethylene glycol was followed by time-resolved EPR spectroscopy. In all reported TR-EPR spectra, except those obtained from the photolysis of 2-nitroresorcinol, the key intermediate N-hydroxy-arylnitroxide radicals (ArNO*OH, 1-4) could be identified unambiguously. In 2-nitroresorcinol, the radical anion (ArNO*O(-), 5) and a sigma iminoxy radical (6) were observed, and a third radical (7) remains unidentified. These observations indicate that two radicalar mechanisms (by H* transfer and by electron transfer) are competing in the photoreduction mechanism. The attribution of the EPR spectra was helped by DFT calculations of the hyperfine coupling constants (hcc's).

Mössbauer Characterization of an Unusual High-Spin Side-On Peroxo−Fe3+ Species in the Active Site of Superoxide Reductase from Desulfoarculus baarsii. Density Functional Calculations on Related Models

Superoxide reductase (SOR) is an Fe protein that catalyzes the reduction of superoxide to give H(2)O(2). Recently, the mutation of the Glu47 residue into alanine (E47A) in the active site of SOR from Desulfoarculus baarsii has allowed the stabilization of an iron-peroxo species when quickly reacted with H(2)O(2) [Mathé et al. (2002) J. Am. Chem. Soc. 124, 4966-4967]. To further investigate this non-heme peroxo-iron species, we have carried out a Mössbauer study of the (57)Fe-enriched E47A SOR from D. baarsii reacted quickly with H(2)O(2). Considering the Mössbauer data, we conclude, in conjunction with the other spectroscopic data available and with the results of density functional calculations on related models, that this species corresponds to a high-spin side-on peroxo-Fe(3+) complex. This is one of the first examples of such a species in a biological system for which Mössbauer parameters are now available: delta(/Fe) = 0.54 (1) mm/s, DeltaE(Q) = -0.80 (5) mm/s, and the asymmetry parameter eta = 0.60 (5) mm/s. The Mössbauer and spin Hamiltonian parameters have been evaluated on a model from the side-on peroxo complex (model 2) issued from the oxidized iron center in SOR from Pyrococcus furiosus, for which structural data are available in the literature [Yeh et al. (2000) Biochemistry 39, 2499-2508]. For comparison, similar calculations have been carried out on a model derived from 2 (model 3), where the [CH(3)-S](1)(-) group has been replaced by the neutral [NH(3)](0) group [Neese and Solomon (1998) J. Am. Chem. Soc. 120, 12829-12848]. Both models 2 and 3 contain a formally high-spin Fe(3+) ion (i.e., with empty minority spin orbitals). We found, however, a significant fraction ( approximately 0.6 for 2, approximately 0.8 for 3) of spin (equivalently charge) spread over two occupied (minority spin) orbitals. The quadrupole splitting value for 2 is found to be negative and matches quite well the experimental value. The computed quadrupole tensors are rhombic in the case of 2 and axial in the case of 3. This difference originates directly from the presence of the thiolate ligand in 2. A correlation between experimental isomer shifts for Fe(3+) mononuclear complexes with computed electron densities at the iron nucleus has been built and used to evaluate the isomer shift values for 2 and 3 (0.56 and 0.63 mm/s, respectively). A significant increase of isomer shift value is found upon going from a methylthiolate to a nitrogen ligand for the Fe(3+) ion, consistent with covalency effects due to the presence of the axial thiolate ligand. Considering that the isomer shift value for 3 is likely to be in the 0.61-0.65 mm/s range [Horner et al. (2002) Eur. J. Inorg. Chem., 3278-3283], the isomer shift value for a high-spin eta(2)-O(2) Fe(3+) complex with an axial thiolate group can be estimated to be in the 0.54-0.58 mm/s range. The occurrence of a side-on peroxo intermediate in SOR is discussed in relation to the recent data published for a side-on peroxo-Fe(3+) species in another biological system [Karlsson et al. (2003) Science 299, 1039-1042].

Correlation between the MagneticgTensors and the Local Cysteine Geometries for a Series of Reduced [2Fe−2S*] Protein Clusters. A Quantum Chemical Density Functional Theory and Structural Analysis

We relied on the density functional theory (DFT) to study the electronic structure of the [2Fe-2S*](SH)4 model of the active site of 2Fe ferredoxins and other proteins containing reduced [2Fe-2S*] clusters. The two (Fe(3+)-Fe(2+)-S-H) dihedral angles Omega1 and Omega2 defined for the two ligands on the ferrous side were allowed to vary, while the two other (Fe(2+)-Fe(3+)-S-H) angles Omega3 and Omega4 on the ferric side were kept constant. The Landé (g), magnetic hyperfine, and quadrupole tensors for two geometries, C2 (Omega1 = Omega2) and Cs (Omega1 = -Omega2), were calculated. To apply our model to the actual proteins, we listed all of the crystallographic structures available for the [2Fe-2S*] systems. A classification of these proteins, based on the four dihedral angles [Omega(i)](i=1-4), separates them into three main classes. The main structural feature of the first class (Omega1 approximately Omega2), with an average dihedral angle Omega(av) = (Omega1 + Omega2)/2 comprised between 115 degrees and 150 degrees, corresponds to a local ferrous C2 geometry (rather than C2nu, as previously assumed by Bertrand and Gayda: Biochim. Biophys. Acta 1979, 579, 107). We then established a direct correlation between the three principal g values and Omega(av). It is the first time that such a link has been made between the spectroscopic and structural parameters, a link, moreover, fully rationalized by our DFT calculations. We finally point out the basic differences between our C2 results with those of the C2nu phenomenological model proposed in the late 1970s by Bertrand and Gayda.

An approach based on quantum chemistry calculations and structural analysis of a [2Fe-2S] ferredoxin that reveal a redox-linked switch in the electron-transfer process to the Fd-NADP+ reductase

[2Fe-2S] ferredoxins act as electron carriers in photosynthesis by mediating the transfer of electrons from photosystem I to various enzymes such as ferredoxin:NADP(+):reductase (FNR). We have analyzed by density functional theory the possible variations of the electronic properties of the [2Fe-2S] ferredoxin, from the cyanobacterium Anabaena, depending on the redox-linked structural changes observed by X-ray diffraction at atomic resolution (Morales, R.; et al. Biochemistry 1999, 38, 15764-15773). The present results point out a specific and concerted role of Ser47, Phe65, and Glu94 located at the molecule surface, close to the iron-sulfur cluster. These residues were already known to be crucial for efficient electron transfer to FNR (e.g., Hurley, J. K.; et al. Biochemistry 1997, 36, 11100-11117). Our calculations suggest that the Glu94 carboxylate negative charge regulates the electron charge delocalization between the Ser47 CO group and the Phe65 aromatic ring, depending on the redox state. The Glu94 carboxylate is stabilized by a strong hydrogen bond implicating a hydroxyl-containing side chain (i.e., Ser or Thr) at location 47. We propose that the Phe65 ring acts as an intermediary carrier receiving the reducing electron prior to its transfer from the reduced Fd to FNR, in view of its central role in the Fd-FNR interaction.

Single-crystal (57)Fe Q-band ENDOR study of the 4 iron-4 sulfur cluster in its reduced [4Fe-4S](1+) state

(57)Fe Q-band ENDOR has been used to study the [4Fe-4S](1+) state created by gamma irradiation of single crystals of the synthetic model compound [N(C(2)H(5))(4)](2)[Fe(4)S(4)(SCH(2)C(6)H(5))(4)] enriched in (57)Fe. This compound is an excellent biomimetic model of the active sites of many 4 iron-4 sulfur proteins, enabling detailed and systematic studies of its oxidized [4Fe-4S](3+) and reduced [4Fe-4S](1+) paramagnetic states. Taking advantage of the fact that Q-band ENDOR, in contrast with X-Band ENDOR, allows for a very good separation of the (57)Fe transitions from those of the protons, the complete hyperfine tensors of the four iron atoms for the [4Fe-4S](1+) species has been measured with precision. For each iron atom, the electron orbital and electron spin isotropic contributions have been determined separately. Moreover, it is remarkable that two (57)Fe hyperfine tensors attributed to the ferrous pair of iron atoms are very different. In effect, one tensor presents a much larger anisotropic part and a much smaller isotropic part than those of the other. This difference has been interpreted in terms of a differential electron orbital hyperfine interaction among the two ferrous ions.