ENDOR Study Research Articles

Photoinduced EPR and ENDOR studies of the divacancies and nitrogen-vacancy defects in silicon carbide

Photoinduced EPR and ENDOR studies of the divacancies and nitrogen-vacancy defects in silicon carbide

"Rabi oscillations and ENDOR study of trivalent gadolinium ion in LiYF4 crystal "

"Rabi oscillations and ENDOR study of trivalent gadolinium ion in LiYF4 crystal "

14N Hyperfine and nuclear interactions of axial and basal NV centers in 4H-SiC: A high frequency (94 GHz) ENDOR study

The nitrogen-vacancy (NV) centers (NCVSi)− in 4H silicon carbide (SiC) constitute an ensemble of spin S = 1 solid state qubits interacting with the surrounding 14N and 29Si nuclei. As quantum applications based on a polarization transfer from the electron spin to the nuclei require the knowledge of the electron–nuclear interaction parameters, we have used high-frequency (94 GHz) electron–nuclear double resonance spectroscopy combined with first-principles density functional theory to investigate the hyperfine and nuclear quadrupole interactions of the basal and axial NV centers. We observed that the four inequivalent NV configurations (hk, kh, hh, and kk) exhibit different electron–nuclear interaction parameters, suggesting that each NV center may act as a separate optically addressable qubit. Finally, we rationalized the observed differences in terms of distinctions in the local atomic structures of the NV configurations. Thus, our results provide the basic knowledge for an extension of quantum protocols involving the 14N nuclear spin.

Coordination of the Copper Centers in Particulate Methane Monooxygenase: Comparison between Methanotrophs and Characterization of the CuC Site by EPR and ENDOR Spectroscopies.

In nature, methane is oxidized to methanol by two enzymes, the iron-dependent soluble methane monooxygenase (sMMO) and the copper-dependent particulate MMO (pMMO). While sMMO's diiron metal active site is spectroscopically and structurally well-characterized, pMMO's copper sites are not. Recent EPR and ENDOR studies have established the presence of two monocopper sites, but the coordination environment of only one has been determined, that within the PmoB subunit and denoted CuB. Moreover, this recent work only focused on a type I methanotrophic pMMO, while previous observations of the type II enzyme were interpreted in terms of the presence of a dicopper site. First, this report shows that the type II Methylocystis species strain Rockwell pMMO, like the type I pMMOs, contains two monocopper sites and that its CuB site has a coordination environment identical to that of type I enzymes. As such, for the full range of pMMOs this report completes the refutation of prior and ongoing suggestions of multicopper sites. Second, and of primary importance, EPR/ENDOR measurements (a) for the first time establish the coordination environment of the spectroscopically observed site, provisionally denoted CuC, in both types of pMMO, thereby (b) establishing the assignment of this site observed by EPR to the crystallographically observed metal-binding site in the PmoC subunit. Finally, these results further indicate that CuC is the likely site of biological methane oxidation by pMMO, a conclusion that will serve as a foundation for proposals regarding the mechanism of this reaction.

High-Field Pulsed ENDOR with Intra-cavity Radiofrequency Coil

This study compares the performance of two coil configurations for W-band pulsed ENDOR using a setup with both a radiofrequency ‘hairpin’ coil internal to a microwave non-radiative resonator and Helmholtz-like coils external to the resonator. Evaluation of the different coil performances is achieved via the ENDOR study of two model systems. The efficiencies of the coil configurations are first investigated numerically, showing that a higher radiofrequency current-to-magnetic field conversion factor can be achieved with the intra-cavity coil, with a similar radiofrequency magnetic field uniformity. This result is then confirmed by the broadband ENDOR spectra acquired with the two coil arrangements. A gain in the signal-to-noise ratio enabled by the internal coil of about a factor 10 was observed. In some cases, the high conversion factor of the intra-cavity coil led to a saturation of the ENDOR transitions. The possibility to implement a similar intra-cavity radiofrequency coil configuration in higher field spectrometers is finally discussed.

Isolation and Study of Ruthenium-Cobalt Oxo Cubanes Bearing a High-Valent, Terminal RuV-Oxo with Significant Oxyl Radical Character.

High-valent RuV-oxo intermediates have long been proposed in catalytic oxidation chemistry, but investigations into their electronic and chemical properties have been limited due to their reactive nature and rarity. The incorporation of Ru into the [Co3O4] subcluster via the single-step assembly reaction of CoII(OAc)2(H2O)4 (OAc = acetate), perruthenate (RuO4-), and pyridine (py) yielded an unprecedented Ru(O)Co3(μ3-O)4(OAc)4(py)3 cubane featuring an isolable, yet reactive, RuV-oxo moiety. EPR, ENDOR, and DFT studies reveal a valence-localized [RuV(S = 1/2)CoIII3(S = 0)O4] configuration and non-negligible covalency in the cubane core. Significant oxyl radical character in the RuV-oxo unit is experimentally demonstrated by radical coupling reactions between the oxo cubane and both 2,4,6-tri-tert-butylphenoxyl and trityl radicals. The oxo cubane oxidizes organic substrates and, notably, reacts with water to form an isolable μ-oxo bis-cubane complex [(py)3(OAc)4Co3(μ3-O)4Ru]-O-[RuCo3(μ3-O)4(OAc)4(py)3]. Redox activity of the RuV-oxo fragment is easily tuned by the electron-donating ability of the distal pyridyl ligand set at the Co sites demonstrating strong electronic communication throughout the entire cubane cluster. Natural bond orbital calculations reveal cooperative orbital interactions of the [Co3O4] unit in supporting the RuV-oxo moiety via a strong π-electron donation.

High-Resolution ENDOR Spectroscopy Combined with Quantum Chemical Calculations Reveals the Structure of Nitrogenase Janus Intermediate E4(4H).

We have shown that the key state in N2 reduction to two NH3 molecules by the enzyme nitrogenase is E4(4H), the "Janus" intermediate, which has accumulated four [e-/H+] and is poised to undergo reductive elimination of H2 coupled to N2 binding and activation. Initial 1H and 95Mo ENDOR studies of freeze-trapped E4(4H) revealed that the catalytic multimetallic cluster (FeMo-co) binds two Fe-bridging hydrides, [Fe-H-Fe]. However, the analysis failed to provide a satisfactory picture of the relative spatial relationships of the two [Fe-H-Fe]. Our recent density functional theory (DFT) study yielded a lowest-energy form, denoted as E4(4H)(a), with two parallel Fe-H-Fe planes bridging pairs of "anchor" Fe on the Fe2,3,6,7 face of FeMo-co. However, the relative energies of structures E4(4H)(b), with one bridging and one terminal hydride, and E4(4H)(c), with one pair of anchor Fe supporting two bridging hydrides, were not beyond the uncertainties in the calculation. Moreover, a structure of V-dependent nitrogenase resulted in a proposed structure analogous to E4(4H)(c), and additional structures have been proposed in the DFT studies of others. To resolve the nature of hydride binding to the Janus intermediate, we performed exhaustive, high-resolution CW-stochastic 1H-ENDOR experiments using improved instrumentation, Mims 2H ENDOR, and a recently developed pulsed-ENDOR protocol ("PESTRE") to obtain absolute hyperfine interaction signs. These measurements are coupled to DFT structural models through an analytical point-dipole Hamiltonian for the hydride electron-nuclear dipolar coupling to its "anchoring" Fe ions, an approach that overcomes limitations inherent in both experimental interpretation and computational accuracy. The result is the freeze-trapped, lowest-energy Janus intermediate structure, E4(4H)(a).

Characterization of the Earliest Intermediate of Fe-N2Protonation: CW and Pulse EPR Detection of an Fe-NNH Species and Its Evolution to Fe-NNH2+

Iron diazenido species (Fe(NNH)) have been proposed as the earliest intermediates of catalytic N2-to-NH3 conversion (N2RR) mediated by synthetic iron complexes and relatedly as intermediates of N2RR by nitrogenase enzymes. However, direct identification of such iron species, either during or independent of catalysis, has proven challenging owing to their high degree of instability. The isolation of more stable silylated diazenido analogues, Fe(NNSiR3), and also of further downstream intermediates (e.g., Fe(NNH2)), nonetheless points to Fe(NNH) as the key first intermediate of protonation in synthetic systems. Herein we show that low-temperature protonation of a terminally bound Fe-N2- species, supported by a bulky trisphosphinoborane ligand (ArP3B), generates an S = 1/2 terminal Fe(NNH) species that can be detected and characterized by continuous-wave (CW) and pulse EPR techniques. The 1H-hyperfine for ArP3BFe(NNH) derived from the presented ENDOR studies is diagnostic for the distally bound H atom ( aiso = 16.5 MHz). The Fe(NNH) species evolves further to cationic [Fe(NNH2)]+ in the presence of additional acid, the latter being related to a previously characterized [Fe(NNH2)]+ intermediate of N2RR mediated by a far less encumbered iron tris(phosphine)borane catalyst. While catalysis is suppressed in the present sterically very crowded system, N2-to-NH3 conversion can nevertheless be demonstrated. These observations in sum add support to the idea that Fe(NNH) plays a central role as the earliest intermediate of Fe-mediated N2RR in a synthetic system.

Group III Acceptors with Shallow and Deep Levels in Silicon Carbide: ESR and ENDOR Studies

Results of investigations of Group III acceptors (B, Al, and Ga) in crystals of silicon carbide using the most informative electron spin resonance and electron nuclear double resonance methods are presented. Structural models of the acceptors with shallow and deep levels are considered. In addition to the data obtained earlier, studies using high-frequency magnetic resonance were obtained, which allowed revealing orthorhombic deviations from the axial symmetry for the deep acceptors; theoretical analysis explains experimentally found shifts of g factors for the deep acceptors arising due to the orthorhombic deviations, which appear probably due to the Jahn–Teller effect.

Möbius–Hückel Topology Switching in Expanded Porphyrins: EPR, ENDOR, and DFT Studies of Doublet and Triplet Open-Shell Systems

The one-sided Mobius band topology with its characteristic 180° twist has fascinated and inspired philosophers, artists and scientists since a long time. On the molecular level, only in the last 13 years a few chemistry groups succeeded to artificially create novel compounds with Mobius symmetry by theory-based molecular design and elaborate chemical synthesis. The interest in molecules with Mobius band symmetry was greatly stimulated in 1964 by a theoretical paper by Edgar Heilbronner from the ETH Zurich. He predicted that sufficiently large [n]annulenes with a closed-shell electron configuration of 4n π-electrons should allow for sufficient π-overlap stabilization to be synthesizable by twisting them into the Mobius topology of their hydrocarbon skeleton. In 2003, the first synthesis of an aromatic Mobius annulene was accomplished by Rainer Herges and co-workers in Kiel. In 2007, Lechoslaw Latos-Grazynski and co-workers in Wroclaw succeeded in synthesizing free-base di-p-benzi (Yoneda et al., Angew Chem Int Ed 53: 13169–13173, 2014) hexaphyrin (1.1.1.1.1.1), compound 1, an expanded porphyrin which can dynamically switch between Huckel and Mobius conjugation upon changes of solvent and temperature. Shortly thereafter, in 2008, Atsuhiro Osuka and his co-workers from Kyoto, Seoul and Hyogo published the synthesis of an expanded porphyrin in which metalation triggered the production of molecular twisting and Mobius aromaticity. In this minireview, among other studies also our recent EPR, ENDOR and DFT studies on open-shell states of 1, i.e., on the ground-state radical cation doublet state (total electron spin S = 1/2) and the first excited triplet state (S = 1) are summarized. The review is largely based on a previous joint publication of the current authors with the Latos-Grazynski group on radical cations of 1 (Mobius et al., Phys Chem Chem Phys 17:6644–6652, 2015). The radical cation study was the first one of an open-shell π-system with Mobius topology. In the doublet state, the hyperfine interactions of the unpaired electron spin with specific magnetic nuclei in the molecule was used as a sensitive probe for the electronic structure of the molecule and its symmetry properties. This work has now been extended to state-of-the-art DFT theory studies on photo-excited triplet states of 1. In the open-shell triplet state, besides hyperfine couplings, a change of the zero-field splitting interaction between the two unpaired electron spins is predicted to be a viable sensor for electronic structure changes upon Mobius-to-Huckel topology switching.

Proton Matrix ENDOR Studies on Ca2+-depleted and Sr2+-substituted Manganese Cluster in Photosystem II

Proton matrix ENDOR spectra were measured for Ca(2+)-depleted and Sr(2+)-substituted photosystem II (PSII) membrane samples from spinach and core complexes from Thermosynechococcus vulcanus in the S2 state. The ENDOR spectra obtained were similar for untreated PSII from T. vulcanus and spinach, as well as for Ca(2+)-containing and Sr(2+)-substituted PSII, indicating that the proton arrangements around the manganese cluster in cyanobacterial and higher plant PSII and Ca(2+)-containing and Sr(2+)-substituted PSII are similar in the S2 state, in agreement with the similarity of the crystal structure of both Ca(2+)-containing and Sr(2+)-substituted PSII in the S1 state. Nevertheless, slightly different hyperfine separations were found between Ca(2+)-containing and Sr(2+)-substituted PSII because of modifications of the water protons ligating to the Sr(2+) ion. Importantly, Ca(2+) depletion caused the loss of ENDOR signals with a 1.36-MHz separation because of the loss of the water proton W4 connecting Ca(2+) and YZ directly. With respect to the crystal structure and the functions of Ca(2+) in oxygen evolution, it was concluded that the roles of Ca(2+) and Sr(2+) involve the maintenance of the hydrogen bond network near the Ca(2+) site and electron transfer pathway to the manganese cluster.

Synthesis, Characterization, and Nitrogenase-Relevant Reactions of an Iron Sulfide Complex with a Bridging Hydride.

The FeMoco of nitrogenase is an iron–sulfur cluster with exceptional bond-reducing abilities. ENDOR studies have suggested that E4, the state that binds and reduces N2, contains bridging hydrides as part of the active-site iron-sulfide cluster. However, there are no examples of any isolable iron-sulfide cluster with a hydride, which would test the feasibility of such a species. Here, we describe a diiron sulfide hydride complex that is prepared using a mild method involving C–S cleavage of added thiolate. Its reactions with nitrogenase substrates show that the hydride can act as a base or nucleophile and that reduction can cause the iron atoms to bind N2. These results add experimental support to hydride-based pathways for nitrogenase.

ChemInform Abstract: Chemistry of Carotenoid Neutral Radicals

AbstractReview: 93 refs.

Structure determination of bound nitrogen-based adducts with copper(II) acetylacetonato; an EPR, ENDOR and DFT study.

The adducts of bis(acetylacetonato)–copper(II), [Cu(acac)2], formed with a range of nitrogen heterocycles including pyridine (2), methylpyridines (3,4,5), amino-methylpyridines (6,7) and diazines (8,9,10) were investigated in frozen solution using X-band EPR and 1H ENDOR spectroscopy. The small perturbations to the EPR spin Hamiltonian parameters (g and CuA) were consistent with the axial coordination of the nitrogen bases to Cu(II), and found to be dependent on both the basicity and steric influence of the coordinating substrate. The detailed structure of two adducts was then investigated by angular selective (1)H ENDOR and DFT. For the [Cu(acac)2](pyridine) adduct, axial coordination of the substrate was found to occur via the pyridine nitrogen as expected, producing a characteristic (1)H hyperfine coupling ((H)Ai = −2.6, −2.04, 4.7 MHz; β = 36°; aiso = 0.2 MHz) arising from the ortho-(1)H in the ring 2 or 6 position. These results were confirmed by DFT. However, in the [Cu(acac)2](2-amino-6-methyl-pyridine) adduct, the ENDOR data revealed a substantially different (1)H hyperfine coupling ((H)Ai = −4.52, −3.35, 6.47 MHz; β = 14°; aiso = −0.47 MHz) arising from the –NH2 amino protons. Analysis of this experimentally derived tensor in conjunction with the calculated DFT tensors, revealed that the 2-amino-6-methyl-pyridine substrate binds to Cu(II) via the exocyclic amino pyridine nitrogen, but with a tilt angle of 20° of the pyridine ring away from the geometry optimised structure. These results reveal how important structural information on the coordination geometry of Cu(II) adducts can be obtained by (1)H ENDOR, but only when the complete angular dependency profile of the ENDOR data is thoroughly considered.

Artificially maturated [FeFe] hydrogenase from Chlamydomonas reinhardtii: a HYSCORE and ENDOR study of a non-natural H-cluster.

Hydrogenases are enzymes that catalyze the oxidation of H2 as well as the reduction of protons to form H2. The active site of [FeFe] hydrogenase is referred to as the "H-cluster" and consists of a "classical" [4Fe-4S] cluster connected via a bridging cysteine thiol group to a unique [2Fe]H sub-cluster, containing CN(-) and CO ligands as well as a bidentate azadithiolate ligand. It has been recently shown that the biomimetic [Fe2(adt)(CO)4(CN)2](2-) (adt(2-) = azadithiolate) complex resembling the diiron sub-cluster can be inserted in vitro into the apo-protein of [FeFe] hydrogenase, which contains only the [4Fe-4S] part of the H-cluster, resulting in a fully active enzyme. This synthetic tool allows convenient incorporation of a variety of diiron mimics, thus generating hydrogenases with artificial active sites. [FeFe] hydrogenase from Chlamydomonas reinhardtii maturated with the biomimetic complex [Fe2(pdt)(CO)4(CN)2](2-) (pdt(2-) = propanedithiolate), in which the bridging adt(2-) ligand is replaced by pdt(2-), can be stabilized in a state strongly resembling the active oxidized (Hox) state of the native protein. This state is EPR active and the signal originates from the mixed valence Fe(I)Fe(II) state of the diiron sub-cluster. Taking advantage of the variant with (15)N and (13)C isotope labeled CN(-) ligands we performed HYSCORE and ENDOR studies on this hybrid protein. The (13)C hyperfine couplings originating from both CN(-) ligands were determined and assigned. Only the (15)N coupling from the CN(-) ligand bound to the terminal iron was observed. Detailed orientation selective ENDOR and HYSCORE experiments at multiple field positions enabled the extraction of accurate data for the relative orientations of the nitrogen and carbon hyperfine tensors. These data are consistent with the crystal structure assuming a g-tensor orientation following the local symmetry of the binuclear sub-cluster.

A DFT, X- and W-band EPR and ENDOR Study of Nitrogen-Centered Species in (Nano)Hydroxyapatite

Incorporation of the nitrogen-containing impurities in hydroxyapatite (HAp) powders with the sizes of the crystallites of (20–50) nm was studied using first-principles modeling combined with the multi-frequency (9 and 94 GHz) electron paramagnetic resonance (EPR) methods. It is shown that the observed EPR spectra are undoubtedly due to the presence of the bulk radiation-induced NO3 2− radicals. This conclusion is based on spin-polarized density functional theory calculations of spectroscopic parameters within gauge-including projector augmented wave framework followed by the exact comparison of the simulated EPR and electron–nuclear double resonance spectra with the experimental findings. In addition, a comprehensive analysis of the simulated properties allows us to suggest that the paramagnetic centers preferably occupy PO4 3− sites in the HAp structure.

EPR, ENDOR, and electronic structure studies of the Jahn-Teller distortion in an Fe(V) nitride.

The recently synthesized and isolated low-coordinate FeV nitride complex has numerous implications as a model for high-oxidation states in biological and industrial systems. The trigonal [PhB(tBuIm)3FeV≡N]+ (where (PhB(tBuIm)3– = phenyltris(3-tert-butylimidazol-2-ylidene)), (1) low-spin d3 (S = 1/2) coordination compound is subject to a Jahn–Teller (JT) distortion of its doubly degenerate 2E ground state. The electronic structure of this complex is analyzed by a combination of extended versions of the formal two-orbital pseudo Jahn–Teller (PJT) treatment and of quantum chemical computations of the PJT effect. The formal treatment is extended to incorporate mixing of the two e orbital doublets (30%) that results from a lowering of the idealized molecular symmetry from D3h to C3v through strong “doming” of the Fe–C3 core. Correspondingly we introduce novel DFT/CASSCF computational methods in the computation of electronic structure, which reveal a quadratic JT distortion and significant e–e mixing, thus reaching a new level of synergism between computational and formal treatments. Hyperfine and quadrupole tensors are obtained by pulsed 35 GHz ENDOR measurements for the 14/15N-nitride and the 11B axial ligands, and spectra are obtained from the imidazole-2-ylidene 13C atoms that are not bound to Fe. Analysis of the nitride ENDOR tensors surprisingly reveals an essentially spherical nitride trianion bound to Fe, with negative spin density and minimal charge density anisotropy. The four-coordinate 11B, as expected, exhibits negligible bonding to Fe. A detailed analysis of the frontier orbitals provided by the electronic structure calculations provides insight into the reactivity of 1: JT-induced symmetry lowering provides an orbital selection mechanism for proton or H atom transfer reactivity.

Electronic structure of the oxygen evolving complex in photosystem II, as revealed by55Mn Davies ENDOR studies at 2.5 K

We report the first (55)Mn pulsed ENDOR studies on the S2 state multiline spin ½ centre of the oxygen evolving complex (OEC) in Photosystem II (PS II), at temperatures below 4.2 K. These were performed on highly active samples of spinach PS II core complexes, developed previously in our laboratories for photosystem spectroscopic use, at temperatures down to 2.5 K. Under these conditions, relaxation effects which have previously hindered observation of most of the manganese ENDOR resonances from the OEC coupled Mn cluster are suppressed. (55)Mn ENDOR hyperfine couplings ranging from ∼50 to ∼680 MHz are now seen on the S2 state multiline EPR signal. These, together with complementary high resolution X-band CW EPR measurements and detailed simulations, reveal that at least two and probably three Mn hyperfine couplings with large anisotropy are seen, indicating that three Mn(III) ions are likely present in the functional S2 state of the enzyme. This suggests a low oxidation state paradigm for the OEC (mean Mn oxidation level 3.0 in the S1 state) and unexpected Mn exchange coupling in the S2 state, with two Mn ions nearly magnetically silent. Our results rationalize a number of previous ligand ESEEM/ENDOR studies and labelled water exchange experiments on the S2 state of the photosystem, in a common picture which is closely consistent with recent photo-assembly (Kolling et al., Biophys. J. 2012, 103, 313-322) and large scale computational studies on the OEC (Gatt et al., Angew. Chem., Int. Ed. 2012, 51, 12025-12028, Kurashige et al. Nat. Chem. 2013, 5, 660-666).

2P258 Ca除去とSr置換をしたMnクラスターのENDOR法による研究(18B. 光生物:光合成,ポスター,第52回日本生物物理学会年会(2014年度))

2P258 Ca除去とSr置換をしたMnクラスターのENDOR法による研究(18B. 光生物:光合成,ポスター,第52回日本生物物理学会年会(2014年度))

13C and 63,65Cu ENDOR studies of CO Dehydrogenase from Oligotropha carboxidovorans. Experimental Evidence in Support of a Copper–Carbonyl Intermediate

We report here an ENDOR study of an S = 1/2 intermediate state trapped during reduction of the binuclear Mo/Cu enzyme CO dehydrogenase by CO. ENDOR spectra of this state confirm that the (63,65)Cu nuclei exhibits strong and almost entirely isotropic coupling to the unpaired electron, show that this coupling atypically has a positive sign, aiso = +148 MHz, and indicate an apparently undetectably small quadrupolar coupling. When the intermediate is generated using (13)CO, coupling to the (13)C is observed, with aiso = +17.3 MHz. A comparison with the couplings seen in related, structurally assigned Mo(V) species from xanthine oxidase, in conjunction with complementary computational studies, leads us to conclude that the intermediate contains a partially reduced Mo(V)/Cu(I) center with CO bound at the copper. Our results provide strong experimental support for a reaction mechanism that proceeds from a comparable complex of CO with fully oxidized Mo(VI)/Cu(I) enzyme.