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1.
J Synchrotron Radiat ; 31(Pt 2): 322-327, 2024 Mar 01.
Artículo en Inglés | MEDLINE | ID: mdl-38306299

RESUMEN

X-ray spectroscopy is a valuable technique for the study of many materials systems. Characterizing reactions in situ and operando can reveal complex reaction kinetics, which is crucial to understanding active site composition and reaction mechanisms. In this project, the design, fabrication and testing of an open-source and easy-to-fabricate electrochemical cell for in situ electrochemistry compatible with X-ray absorption spectroscopy in both transmission and fluorescence modes are accomplished via windows with large opening angles on both the upstream and downstream sides of the cell. Using a hobbyist computer numerical control machine and free 3D CAD software, anyone can make a reliable electrochemical cell using this design. Onion-like carbon nanoparticles, with a 1:3 iron-to-cobalt ratio, were drop-coated onto carbon paper for testing in situ X-ray absorption spectroscopy. Cyclic voltammetry of the carbon paper showed the expected behavior, with no increased ohmic drop, even in sandwiched cells. Chronoamperometry was used to apply 0.4 V versus reversible hydrogen electrode, with and without 15 min of oxygen purging to ensure that the electrochemical cell does not provide any artefacts due to gas purging. The XANES and EXAFS spectra showed no differences with and without oxygen, as expected at 0.4 V, without any artefacts due to gas purging. The development of this open-source electrochemical cell design allows for improved collection of in situ X-ray absorption spectroscopy data and enables researchers to perform both transmission and fluorescence simultaneously. It additionally addresses key practical considerations including gas purging, reduced ionic resistance and leak prevention.

2.
J Am Chem Soc ; 146(4): 2593-2603, 2024 Jan 31.
Artículo en Inglés | MEDLINE | ID: mdl-38235653

RESUMEN

Hydrogen fuel cells have drawn increasing attention as one of the most promising next-generation power sources for future automotive transportation. Developing efficient, durable, and low-cost electrocatalysts, to accelerate the sluggish oxygen reduction reaction (ORR) kinetics, is urgently needed to advance fuel cell technologies. Herein, we report on metal-organic frameworks-derived nonprecious dual metal single-atom catalysts (SACs) (Zn/Co-N-C), consisting of Co-N4 and Zn-N4 local structures. These catalysts exhibited superior ORR activity with a half-wave potential (E1/2) of 0.938 V versus RHE (reversible hydrogen electrode) and robust stability (ΔE1/2 = -8.5 mV) after 50k electrochemical cycles. Moreover, this remarkable performance was validated under realistic fuel cell working conditions, achieving a record-high peak power density of ∼1 W cm-2 among the reported SACs for alkaline fuel cells. Operando X-ray absorption spectroscopy was conducted to identify the active sites and reveal catalytic mechanistic insights. The results indicated that the Co atom in the Co-N4 structure was the main catalytically active center, where one axial oxygenated species binds to form an Oads-Co-N4 moiety during the ORR. In addition, theoretical studies, based on a potential-dependent microkinetic model and core-level shift calculations, showed good agreement with the experimental results and provided insights into the bonding of oxygen species on Co-N4 centers during the ORR. This work provides a comprehensive mechanistic understanding of the active sites in the Zn/Co-N-C catalysts and will pave the way for the future design and advancement of high-performance single-site electrocatalysts for fuel cells and other energy applications.

3.
J Am Chem Soc ; 145(37): 20208-20213, 2023 Sep 20.
Artículo en Inglés | MEDLINE | ID: mdl-37677089

RESUMEN

Advances in electrocatalysis research rely heavily on building a thorough mechanistic understanding of catalyst active sites under realistic operating conditions. Only recently have techniques emerged that enable sensitive spectroscopic data collection to distinguish catalytically relevant surface sites from the underlying bulk material under applied potential in the presence of an electrolyte layer. Here, we demonstrate that operando high-energy-resolution fluorescence detected X-ray absorption spectroscopy (HERFD-XAS) is a powerful spectroscopic method which offers critical surface chemistry insights in CO2 electroreduction with sub-electronvolt energy resolution using hard X-rays. Combined with the high surface area-to-volume ratio of 5 nm copper nanoparticles, operando HERFD-XAS allows us to observe with clear evidence the breaking of chemical bonds between the ligands and the Cu surface as part of the ligand desorption process occurring under electrochemical potentials relevant for the CO2 reduction reaction (CO2RR). In addition, the dynamic evolution of oxidation state and coordination number throughout the operation of the nanocatalyst was continuously tracked. With these results in hand, undercoordinated metallic copper nanograins are proposed to be the real active sites in the CO2RR. This work emphasizes the importance of HERFD-XAS compared to routine XAS in catalyst characterization and mechanism exploration, especially in the complicated electrochemical CO2RR.

4.
Sci Adv ; 9(33): eadi5108, 2023 Aug 18.
Artículo en Inglés | MEDLINE | ID: mdl-37585528

RESUMEN

Lithium-sulfur batteries represent an attractive option for energy storage applications. A deeper understanding of the multistep lithium-sulfur reactions and the electrocatalytic mechanisms are required to develop advanced, high-performance batteries. We have systematically investigated the lithium-sulfur redox processes catalyzed by a cobalt single-atom electrocatalyst (Co-SAs/NC) via operando confocal Raman microscopy and x-ray absorption spectroscopy (XAS). The real-time observations, based on potentiostatic measurements, indicate that Co-SAs/NC efficiently accelerates the lithium-sulfur reduction/oxidation reactions, which display zero-order kinetics. Under galvanostatic discharge conditions, the typical stepwise mechanism of long-chain and intermediate-chain polysulfides is transformed to a concurrent pathway under electrocatalysis. In addition, operando cobalt K-edge XAS studies elucidate the potential-dependent evolution of cobalt's oxidation state and the formation of cobalt-sulfur bonds. Our work provides fundamental insights into the mechanisms of catalyzed lithium-sulfur reactions via operando methods, enabling a deeper understanding of electrocatalysis and interfacial dynamics in electrical energy storage systems.

5.
Inorg Chem ; 62(34): 13681-13691, 2023 Aug 28.
Artículo en Inglés | MEDLINE | ID: mdl-37578150

RESUMEN

Valence-to-core X-ray emission spectroscopy (VtC XES) is an emerging technique that uses hard X-rays to probe the valence electronic structure of an absorbing atom. Despite finding varied applications for light elements and first row transition metals, little work has been done on heavier elements such as second and third row transition metals. This lack of application is at least partially due to the relatively low resolution of the data at the high energies required to measure these elements, which obscures the useful chemical information that can be extracted from the lower energy, higher resolution spectra of lighter elements. Herein, we collect data on a set of platinum-containing compounds and demonstrate that the VtC XES resolution can be dramatically enhanced by exciting the platinum atom in resonance with its L3-edge white line absorption. Whereas spectra excited using standard nonresonant absorption well above the Pt L3-edge display broad, unfeatured VtC regions, resonant XES (RXES) spectra have more than twofold improved resolution and are revealed to be rich in chemical information with the ability to distinguish between even closely related species. We further demonstrate that these RXES spectra may be used to selectively probe individual components of a mixture of Pt-containing compounds, establishing this technique as a viable probe for chemically complex samples. Lastly, it is shown that the spectra are interpretable using a molecular orbital framework and may be calculated using density functional theory, thus suggesting resonant excitation as a general strategy for extracting chemically useful information from heavy element VtC spectra.

6.
Nature ; 614(7947): 262-269, 2023 02.
Artículo en Inglés | MEDLINE | ID: mdl-36755171

RESUMEN

Carbon dioxide electroreduction facilitates the sustainable synthesis of fuels and chemicals1. Although Cu enables CO2-to-multicarbon product (C2+) conversion, the nature of the active sites under operating conditions remains elusive2. Importantly, identifying active sites of high-performance Cu nanocatalysts necessitates nanoscale, time-resolved operando techniques3-5. Here, we present a comprehensive investigation of the structural dynamics during the life cycle of Cu nanocatalysts. A 7 nm Cu nanoparticle ensemble evolves into metallic Cu nanograins during electrolysis before complete oxidation to single-crystal Cu2O nanocubes following post-electrolysis air exposure. Operando analytical and four-dimensional electrochemical liquid-cell scanning transmission electron microscopy shows the presence of metallic Cu nanograins under CO2 reduction conditions. Correlated high-energy-resolution time-resolved X-ray spectroscopy suggests that metallic Cu, rich in nanograin boundaries, supports undercoordinated active sites for C-C coupling. Quantitative structure-activity correlation shows that a higher fraction of metallic Cu nanograins leads to higher C2+ selectivity. A 7 nm Cu nanoparticle ensemble, with a unity fraction of active Cu nanograins, exhibits sixfold higher C2+ selectivity than the 18 nm counterpart with one-third of active Cu nanograins. The correlation of multimodal operando techniques serves as a powerful platform to advance our fundamental understanding of the complex structural evolution of nanocatalysts under electrochemical conditions.

7.
J Phys Condens Matter ; 34(34)2022 Jun 22.
Artículo en Inglés | MEDLINE | ID: mdl-35667370

RESUMEN

We report the temperature dependence of the Yb valence in the geometrically frustrated compoundYbB4from 12 to 300 K using resonant x-ray emission spectroscopy at the YbLα1transition. We find that the Yb valence,v, is hybridized between thev = 2 andv = 3 valence states, increasing fromv=2.61±0.01at 12 K tov=2.67±0.01at 300 K, confirming thatYbB4is a Kondo system in the intermediate valence regime. This result indicates that the Kondo interaction inYbB4is substantial, and is likely to be the reason whyYbB4does not order magnetically at low temperature, rather than this being an effect of geometric frustration. Furthermore, the zero-point valence of the system is extracted from our data and compared with other Kondo lattice systems. The zero-point valence seems to be weakly dependent on the Kondo temperature scale, but not on the valence change temperature scaleTv.

8.
Phys Chem Chem Phys ; 23(43): 24780-24788, 2021 Nov 10.
Artículo en Inglés | MEDLINE | ID: mdl-34714314

RESUMEN

Platinum is used extensively as a catalyst for a wide variety of chemical reactions, though its scarcity and price present limitations to expansions of its use. To understand the origin of platinum's versatility-with the goals of both improving the efficiency of existing catalysts and mimicking its reactivity with more abundant metals-the mechanisms of platinum-catalyzed chemical reactions must be understood via structural and spectroscopic characterization of these catalysts under operando conditions. Such data, typically consisting of complex mixtures of species, often prove challenging to interpret, inviting the aid of chemical theory. DFT calculations in particular have proven successful at predicting structural and spectroscopic parameters of transition metal species, though a thorough investigation of how these methods perform for platinum-based complexes has yet to be undertaken. Herein, we evaluated the performance of geometry optimization for five commonly used functionals (BP86, PBE, B3LYP, PBE0, and TPSSh) in combination with various ligand basis sets, relativistic approximations, and solvation and dispersion models. We applied these DFT methods to a training set of 14 platinum-containing complexes with varying sizes, oxidation states, and number and type of ligands and determined that the best-performing method was the PBE0 functional together with the def2-TZVP basis set for the ligand atoms, the ZORA relativistic approximation, and solvation and dispersion corrections. The ability of this DFT methodology to accurately predict metrical parameters was confirmed using two case studies, most notably by comparing the DFT optimized geometry of a previously uncharacterized complex to newly collected EXAFS data, which showed excellent agreement.

9.
Mar Environ Res ; 171: 105457, 2021 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-34482114

RESUMEN

The southern North Sea holds the world's highest concentration of offshore wind farms (OWFs). Northern gannets (Morus bassanus), a species considered at high risk from OWF impacts, show a strong seasonal peak there in November, but it is unclear which populations and age classes are most at risk of collision with wind turbines. We tagged adult and juvenile gannets at the world's largest colony (Bass Rock) and reviewed two sources of survey data for different age classes to study their movements through southern North Sea waters. Tracked birds showed peak numbers in the southern North Sea in mid-October, with much smaller numbers there during November. Adults were distributed throughout the area, including waters close to OWFs, whereas juveniles were confined to the coast. Survey data indicated high proportions of immature gannets in southern North Sea waters, suggesting higher collision risk than for adults. Gannets present in November may be predominantly from colonies further north than Bass Rock.


Asunto(s)
Fuentes Generadoras de Energía , Viento , Animales , Aves , Mar del Norte
10.
ACS Omega ; 6(27): 17203-17216, 2021 Jul 13.
Artículo en Inglés | MEDLINE | ID: mdl-34278107

RESUMEN

Studying the oxygen reduction reaction (ORR) in the alkaline electrolyte has proven to promote better catalytic responses and accessibility to commercialization. Ni-nanowires (NWs) were synthesized via the solvothermal method and modified with Pt using the spontaneous galvanic displacement method to obtain PtNi-NWs. Carbon Vulcan XC-72R (V) was used as the catalyst support, and they were doped with NH3 to obtain PtNi-NWs/V and PtNi-NWs/V-NH3. Their electrocatalytic response for the ORR was tested and PtNi-NWs/V provided the highest specific activity with logarithmic values of 0.707 and 1.01 (mA/cm2 Pt) at 0.90 and 0.85 V versus reversible hydrogen electrode (RHE), respectively. PtNi-NWs showed the highest half-wave potential (E 1/2 = 0.89 V) at 1600 rpm and 12 µgPt/cm2 in 0.1 M KOH at 25.00 ± 0.01 °C. Additionally, the catalysts followed a four-electron pathway according to the Koutecký-Levich analysis. Moreover, durability experiments demonstrated that the PtNi-NW/V performance loss was like that of commercial Pt/V along 10,000 cycles. Electrochemical ORR in situ X-ray absorption spectroscopy results showed that the Pt L3 edge white line in the PtNi-NW catalysts changed while the electrochemical potential was lowered to negatives values, from 1.0 to 0.3 V versus RHE. The Pt/O region in the in situ Fourier transforms remained the same as the potentials were applied, suggesting an alloy formation between Pt and Ni, and Pt/Pt contracted in the presence of Ni. These results provide a better understanding of PtNi-NWs in alkaline electrolytes, suggesting that they are active catalysts for ORR and can be tuned for fuel cell studies.

11.
Biol Rev Camb Philos Soc ; 96(5): 1868-1888, 2021 10.
Artículo en Inglés | MEDLINE | ID: mdl-33978325

RESUMEN

To robustly predict the effects of disturbance and ecosystem changes on species, it is necessary to produce structurally realistic models with high predictive power and flexibility. To ensure that these models reflect the natural conditions necessary for reliable prediction, models must be informed and tested using relevant empirical observations. Pattern-oriented modelling (POM) offers a systematic framework for employing empirical patterns throughout the modelling process and has been coupled with complex systems modelling, such as in agent-based models (ABMs). However, while the production of ABMs has been rising rapidly, the explicit use of POM has not increased. Challenges with identifying patterns and an absence of specific guidelines on how to implement empirical observations may limit the accessibility of POM and lead to the production of models which lack a systematic consideration of reality. This review serves to provide guidance on how to identify and apply patterns following a POM approach in ABMs (POM-ABMs), specifically addressing: where in the ecological hierarchy can we find patterns; what kinds of patterns are useful; how should simulations and observations be compared; and when in the modelling cycle are patterns used? The guidance and examples provided herein are intended to encourage the application of POM and inspire efficient identification and implementation of patterns for both new and experienced modellers alike. Additionally, by generalising patterns found especially useful for POM-ABM development, these guidelines provide practical help for the identification of data gaps and guide the collection of observations useful for the development and verification of predictive models. Improving the accessibility and explicitness of POM could facilitate the production of robust and structurally realistic models in the ecological community, contributing to the advancement of predictive ecology at large.


Asunto(s)
Ecosistema
12.
Mar Environ Res ; 162: 105196, 2020 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-33126111

RESUMEN

There is a pressing need to quantify the risks of renewable energy developments such as offshore wind farms for protected populations. However, assessments are often based on incomplete data, or fail to consider variation in risk between sexes and at different times of year. We tracked northern gannets foraging from the world's largest colony (Bass Rock, Scotland) across five consecutive breeding seasons. We examine how seasonal and sex differences in behaviour affect the collision risk from planned and operational wind farms within their foraging range and assess the likely consequences for long-term population viability. Both sexes made shorter trips during chick-rearing than prior to chick-hatching, spent a greater proportion of time within wind farm sites and had an eight times greater potential collision risk during chick-rearing. Females made longer trips than males at both these times of year, flew higher and spent more time within wind farm sites, leading to three times greater collision risk for females. After accounting for the potential additional mortality from collisions, and assuming that the death of a parent also led to the loss of its offspring, the breeding population was projected to increase by 3.57% (95% CI: 2.16-5.15%) per year, compared with 6.56% (95% CI: 4.59-8.73%) in the absence of turbines, suggesting a negligible effect on population viability. However, additional mortality could result in greater immigration from neighbouring colonies, potentially affecting their viability and highlighting a need for research within a metapopulation framework to assess the impacts of offshore wind developments on vulnerable species across multiple connected sites.


Asunto(s)
Fuentes Generadoras de Energía , Viento , Animales , Demografía , Femenino , Masculino , Escocia , Estaciones del Año
13.
PLoS One ; 15(9): e0238962, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32881932

RESUMEN

[This corrects the article DOI: 10.1371/journal.pone.0223080.].

14.
PLoS One ; 15(7): e0223080, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32639962

RESUMEN

Recent reviews on sexual dichromatism in frogs included Mannophryne trinitatis as the only example they could find of dynamic dichromatism (males turn black when calling) within the family Aromobatidae and found no example of ontogenetic dichromatism in this group. We demonstrate ontogenetic dichromatism in M. trinitatis by rearing post-metamorphic froglets to near maturity: the throats of all individuals started as grey coloured; at around seven weeks, the throat became pale yellow in some, and more strongly yellow as development proceeded; the throats of adults are grey in males and variably bright yellow in females, backed by a dark collar. We demonstrated the degree of throat colour variability by analysing a large sample of females. The red: green (R:G) ratio ranged from ~1.1 to 1.4, reflecting variation from yellow to yellow/orange, and there was also variation in the tone and width of the dark collar, and in the extent to which the yellow colouration occurred posterior to the collar. Female M. trinitatis are known to be territorial in behaviour. We show a positive relationship between throat colour (R:G ratio) and escape performance, as a proxy for quality. Our field observations on Tobago's M. olmonae showed variability in female throat colour and confirmed that males in this species also turn black when calling. Our literature review of the 20 Mannophryne species so far named showed that all females have yellow throats with dark collars, and that male colour change to black when calling has been reported in eight species; in the remaining 12 species, descriptions of males calling are usually lacking so far. We predict that both dynamic and ontogenetic sexual dichromatism are universal in this genus and provide discussion of the ecological role of dichromatism in this genus of predominantly diurnal, non-toxic frogs, with strong paternal care of offspring.


Asunto(s)
Anuros/fisiología , Caracteres Sexuales , Animales , Anuros/crecimiento & desarrollo , Conducta Animal , Color , Femenino , Masculino , Faringe/fisiología
15.
J Inorg Biochem ; 203: 110877, 2020 02.
Artículo en Inglés | MEDLINE | ID: mdl-31710865

RESUMEN

Ferritin-like carboxylate-bridged non-heme diiron enzymes activate O2 for a variety of difficult reactions throughout nature. These reactions often begin by abstraction of hydrogen from strong CH bonds. The enzymes activate O2 at their diferrous cofactors to form canonical diferric peroxo intermediates, with a range of possible coordination modes. Herein, we explore the ability of high-energy resolution fluorescence detected X-ray absorption spectroscopy (HERFD XAS) to provide insight into the nature of peroxo level intermediates in non-heme diiron proteins. Freeze quenched (FQ) peroxo intermediates from p-aminobenzoate N-oxygenase (AurF), aldehyde-deformylating oxygenase (ADO), and the ß subunit of class Ia ribonucleotide reductase from Escherichia coli (Ecß) are investigated. All three intermediates are proposed to adopt different peroxo binding modes, and each exhibit different Fe Kα HERFD XAS pre-edge features and intensities. As these FQ-trapped samples consist of multiple species, deconvolution of HERFD XAS spectra based on speciation, as determined by Mössbauer spectroscopy, is also necessitated - yielding 'pure' diferric peroxo HERFD XAS spectra from dilute protein samples. Finally, the impact of a given peroxo coordination mode on the HERFD XAS pre-edge energy and intensity is evaluated through time-dependent density functional theory (TDDFT) calculations of the XAS spectra on a series of hypothetical model complexes, which span a full range of possible peroxo coordination modes to a diferric core. The utility of HERFD XAS for future studies of enzymatic intermediates is discussed.


Asunto(s)
Proteínas Bacterianas/química , Hierro/química , Oxigenasas/química , Peróxidos/química , Ribonucleótido Reductasas/química , Teoría Funcional de la Densidad , Escherichia coli/enzimología , Proteínas de Escherichia coli/química , Modelos Químicos , Oxidación-Reducción , Oxígeno/química , Espectroscopía de Absorción de Rayos X
16.
J Am Chem Soc ; 141(38): 15153-15165, 2019 09 25.
Artículo en Inglés | MEDLINE | ID: mdl-31475820

RESUMEN

Iron(II)- and 2-oxoglutarate-dependent (Fe/2OG) oxygenases generate iron(IV)-oxo (ferryl) intermediates that can abstract hydrogen from aliphatic carbons (R-H). Hydroxylation proceeds by coupling of the resultant substrate radical (R•) and oxygen of the Fe(III)-OH complex ("oxygen rebound"). Nonhydroxylation outcomes result from different fates of the Fe(III)-OH/R• state; for example, halogenation results from R• coupling to a halogen ligand cis to the hydroxide. We previously suggested that halogenases control substrate-cofactor disposition to disfavor oxygen rebound and permit halogen coupling to prevail. Here, we explored the general implication that, when a ferryl intermediate can ambiguously target two substrate carbons for different outcomes, rebound to the site capable of the alternative outcome should be slower than to the adjacent, solely hydroxylated site. We evaluated this prediction for (i) the halogenase SyrB2, which exclusively hydroxylates C5 of norvaline appended to its carrier protein but can either chlorinate or hydroxylate C4 and (ii) two bifunctional enzymes that normally hydroxylate one carbon before coupling that oxygen to a second carbon (producing an oxacycle) but can, upon encountering deuterium at the first site, hydroxylate the second site instead. In all three cases, substrate hydroxylation incorporates a greater fraction of solvent-derived oxygen at the site that can also undergo the alternative outcome than at the other site, most likely reflecting an increased exchange of the initially O2-derived oxygen ligand in the longer-lived Fe(III)-OH/R• states. Suppression of rebound may thus be generally important for nonhydroxylation outcomes by these enzymes.


Asunto(s)
Compuestos Ferrosos/metabolismo , Ácidos Cetoglutáricos/metabolismo , Oxígeno/metabolismo , Oxigenasas/metabolismo , Compuestos Ferrosos/química , Ácidos Cetoglutáricos/química , Estructura Molecular , Oxígeno/química , Oxigenasas/química , Estereoisomerismo
17.
Angew Chem Int Ed Engl ; 57(39): 12754-12758, 2018 09 24.
Artículo en Inglés | MEDLINE | ID: mdl-30075052

RESUMEN

Proton transfer reactions are of central importance to a wide variety of biochemical processes, though determining proton location and monitoring proton transfers in biological systems is often extremely challenging. Herein, we use two-color valence-to-core X-ray emission spectroscopy (VtC XES) to identify protonation events across three oxidation states of the O2 -activating, radical-initiating manganese-iron heterodinuclear cofactor in a class I-c ribonucleotide reductase. This is the first application of VtC XES to an enzyme intermediate and the first simultaneous measurement of two-color VtC spectra. In contrast to more conventional methods of assessing protonation state, VtC XES is a more direct probe applicable to a wide range of metalloenzyme systems. These data, coupled to insight provided by DFT calculations, allow the inorganic cores of the MnIV FeIV and MnIV FeIII states of the enzyme to be assigned as MnIV (µ-O)2 FeIV and MnIV (µ-O)(µ-OH)FeIII , respectively.


Asunto(s)
Proteínas Bacterianas/metabolismo , Ribonucleótido Reductasas/metabolismo , Espectrometría por Rayos X , Proteínas Bacterianas/química , Chlamydia trachomatis/enzimología , Teoría Funcional de la Densidad , Compuestos Férricos/química , Iones/química , Hierro/química , Manganeso/química , Protones , Ribonucleótido Reductasas/química
19.
Biochemistry ; 57(18): 2679-2693, 2018 05 08.
Artículo en Inglés | MEDLINE | ID: mdl-29609464

RESUMEN

A ribonucleotide reductase (RNR) from Flavobacterium johnsoniae ( Fj) differs fundamentally from known (subclass a-c) class I RNRs, warranting its assignment to a new subclass, Id. Its ß subunit shares with Ib counterparts the requirements for manganese(II) and superoxide (O2-) for activation, but it does not require the O2--supplying flavoprotein (NrdI) needed in Ib systems, instead scavenging the oxidant from solution. Although Fj ß has tyrosine at the appropriate sequence position (Tyr 104), this residue is not oxidized to a radical upon activation, as occurs in the Ia/b proteins. Rather, Fj ß directly deploys an oxidized dimanganese cofactor for radical initiation. In treatment with one-electron reductants, the cofactor can undergo cooperative three-electron reduction to the II/II state, in contrast to the quantitative univalent reduction to inactive "met" (III/III) forms seen with I(a-c) ßs. This tendency makes Fj ß unusually robust, as the II/II form can readily be reactivated. The structure of the protein rationalizes its distinctive traits. A distortion in a core helix of the ferritin-like architecture renders the active site unusually open, introduces a cavity near the cofactor, and positions a subclass-d-specific Lys residue to shepherd O2- to the Mn2II/II cluster. Relative to the positions of the radical tyrosines in the Ia/b proteins, the unreactive Tyr 104 of Fj ß is held away from the cofactor by a hydrogen bond with a subclass-d-specific Thr residue. Structural comparisons, considered with its uniquely simple mode of activation, suggest that the Id protein might most closely resemble the primordial RNR-ß.


Asunto(s)
Flavoproteínas/química , Manganeso/química , Ribonucleótido Reductasas/química , Superóxidos/química , Catálisis , Dominio Catalítico , Flavobacterium/química , Flavobacterium/enzimología , Flavoproteínas/metabolismo , Hierro/química , Oxidación-Reducción , Oxígeno/química , Ribonucleótido Reductasas/clasificación , Ribonucleótido Reductasas/metabolismo , Tirosina/química
20.
Inorg Chem ; 56(21): 13382-13389, 2017 Nov 06.
Artículo en Inglés | MEDLINE | ID: mdl-28960972

RESUMEN

The iron(II)- and 2-(oxo)glutarate-dependent (Fe/2OG) oxygenases catalyze an array of challenging transformations via a common iron(IV)-oxo (ferryl) intermediate, which in most cases abstracts hydrogen (H•) from an aliphatic carbon of the substrate. Although it has been shown that the relative disposition of the Fe-O and C-H bonds can control the rate of H• abstraction and fate of the resultant substrate radical, there remains a paucity of structural information on the actual ferryl states, owing to their high reactivity. We demonstrate here that the stable vanadyl ion [(VIV-oxo)2+] binds along with 2OG or its decarboxylation product, succinate, in the active site of two different Fe/2OG enzymes to faithfully mimic their transient ferryl states. Both ferryl and vanadyl complexes of the Fe/2OG halogenase, SyrB2, remain stably bound to its carrier protein substrate (l-aminoacyl-S-SyrB1), whereas the corresponding complexes harboring transition metals (Fe, Mn) in lower oxidation states dissociate. In the well-studied taurine:2OG dioxygenase (TauD), the disposition of the substrate C-H bond relative to the vanadyl ion defined by pulse electron paramagnetic resonance methods is consistent with the crystal structure of the reactant complex and computational models of the ferryl state. Vanadyl substitution may thus afford access to structural details of the key ferryl intermediates in this important enzyme class.


Asunto(s)
Hierro/química , Proteínas de Hierro no Heme/química , Oxidorreductasas/química , Vanadatos/química , Proteínas Portadoras/química , Dominio Catalítico , Oxigenasas de Función Mixta/química , Oxidación-Reducción , Ácido Succínico/química , Taurina/química
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