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3-mercaptopropionate (3MPA) dioxygenase (MDO) is a mononuclear nonheme iron enzyme that catalyzes the O2-dependent oxidation of thiol-bearing substrates to yield the corresponding sulfinic acid. MDO is a member of the cysteine dioxygenase family of small molecule thiol dioxygenases and thus shares a conserved sequence of active site residues (Serine-155, Histidine-157, and Tyrosine-159), collectively referred to as the SHY-motif. It has been demonstrated that these amino acids directly interact with the mononuclear Fe-site, influencing steady-state catalysis, catalytic efficiency, O2-binding, and substrate coordination. However, the underlying mechanism by which this is accomplished is poorly understood. Here, pulsed electron paramagnetic resonance spectroscopy [1H Mims electron nuclear double resonance spectroscopy] is applied to validate density functional theory computational models for the MDO Fe-site simultaneously coordinated by substrate and nitric oxide (NO), (3MPA/NO)-MDO. The enhanced resolution provided by electron nuclear double resonance spectroscopy allows for direct observation of Fe-bound substrate conformations and H-bond donation from Tyr159 to the Fe-bound NO ligand. Further inclusion of SHY-motif residues within the validated model reveals a distinct channel restricting movement of the Fe-bound NO-ligand. It has been argued that the iron-nitrosyl emulates the structure of potential Fe(III)-superoxide intermediates within the MDO catalytic cycle. While the merit of this assumption remains unconfirmed, the model reported here offers a framework to evaluate oxygen binding at the substrate-bound Fe-site and possible reaction mechanisms. It also underscores the significance of hydrogen bonding interactions within the enzymatic active site.
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Dominio Catalítico , Dioxigenasas , Modelos Moleculares , Ácido 3-Mercaptopropiónico/química , Catálisis , Dioxigenasas/química , Dioxigenasas/metabolismo , Espectroscopía de Resonancia por Spin del Electrón , Hierro/metabolismo , Óxido Nítrico/metabolismo , Oxígeno/metabolismo , Estructura Terciaria de ProteínaRESUMEN
Conformational changes of catalytically-important structural elements are a key feature of the regulation mechanisms of protein kinases and are important for dictating inhibitor binding modes and affinities. The lack of widely applicable methods for tracking kinase conformational changes in solution has hindered our understanding of kinase regulation and our ability to design conformationally selective inhibitors. Here we provide an overview of two recently developed methods that detect conformational changes of the regulatory activation loop and αC-helix of kinases and that yield complementary information about allosteric mechanisms. An intramolecular Förster resonance energy transfer-based approach provides a scalable platform for detecting and classifying structural changes in high-throughput, as well as quantifying ligand binding cooperativity, shedding light on the energetics governing allostery. The pulsed electron paramagnetic resonance technique double electron-electron resonance provides lower throughput but higher resolution information on structural changes that allows for unambiguous assignment of conformational states and quantification of population shifts. Together, these methods are shedding new light on kinase regulation and drug interactions and providing new routes for the identification of novel kinase inhibitors and allosteric modulators.
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Transferencia Resonante de Energía de Fluorescencia , Conformación Proteica , Proteínas Quinasas , Espectroscopía de Resonancia por Spin del Electrón/métodos , Proteínas Quinasas/química , Proteínas Quinasas/metabolismo , Regulación Alostérica , Inhibidores de Proteínas Quinasas/química , Inhibidores de Proteínas Quinasas/farmacología , Humanos , Unión Proteica , Modelos MolecularesRESUMEN
Actinides are inherently radioactive; thus, ionizing radiation is emitted by these elements can have profound effects on its surrounding chemical environment through the formation of free radical species. While previous work has noted that the presence of free radicals in the system impacts the redox state of the actinides, there is little atomistic understanding of how these metal cations interact with free radicals. Herein, we explore the effects of radiation (UV and γ) on three U(VI) trinitrate complexes, M[UO2(NO3)3] (where M=K+, Rb+, Cs+), and their respective nitrate salts in the solid state via electron paramagnetic resonance (EPR) and Raman spectroscopy paired with Density Functional Theory (DFT) methods. We find that the alkali salts form nitrate radicals under UV and γ irradiation, but also note the presence of additional degradation products. M[UO2(NO3)3] solids also form nitrate radicals and additional DFT calculations indicate the species corresponds to a change from the bidentate bound nitrate anion into a monodentate NO3 ⢠radical. Computational studies also highlight the need to include the second sphere coordination environment around the [UO2(NO3)3]0,1 species to gain agreement between the experimental and predicted EPR signatures.
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Being a low-toxic and hydrophilic representative of TAM, OX063 has shown its suitability for in-vivo and in-cell EPR experiments and design of spin labels. Using 13C labeling, we investigated the course of oxidative degradation of OX063 into quinone-methide (QM) under the influence of superoxide as well as further thiol-promoted reduction of QM into TAM radical, which formally corresponds to substitution of a carboxyl function by a hydroxyl group. We found these transformations being quantitative in model reactions mimicking specific features of biological media and confirmed the presence of these reactions in the blood and liver homogenate of mice in vitro. The emergence of the trityl with the hydroxyl group can be masked by an initial TAM in EPR spectra and may introduce distortions into EPR-derived oximetry data if they have been obtained for objects under hypoxia. 13C labeling allows one to detect its presence, considering its different hyperfine splitting constant on 13C1 (2.04 mT) as compared to OX063 (2.30 mT). The potential involvement of these reactions should be considered when using TAM in spin-labeling of biopolymers intended for subsequent EPR experiments, as well as in the successful application of TAM in experiments in vivo and in cell.
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Respiratory complex I (R-CI) is an essential enzyme in the mitochondrial electron transport chain but also a major source of reactive oxygen species (ROS), which are implicated in neurodegenerative diseases and ageing. While the mechanism of ROS production by R-CI is well-established, the feedback of ROS on R-CI activity is poorly understood. Here, we perform EPR spectroscopy on R-CI incorporated in artificial membrane vesicles to reveal that ROS (particularly hydroxyl radicals) reduce R-CI activity by making the membrane more polar and by increasing its hydrogen bonding capability. Moreover, the mechanism that we have uncovered reveals that the feedback of ROS on R-CI activity via the membrane is transient and not permanent; lipid peroxidation is negligible for the levels of ROS generated under these conditions. Our successful use of modular proteoliposome systems in conjunction with EPR spectroscopy and other biophysical techniques is a powerful approach for investigating ROS effects on other membrane proteins.
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New cobalt(II)-based complexes with [N2O2] coordination formed by two bis-chelate ligands were synthesized and characterized by a multi-technique approach. The complexes possess an easy-axis anisotropy (D < 0) and magnetic measurements show a field-induced slow relaxation of magnetization. The spin-reversal barriers, i.e., the splitting of the two lowest Kramers doublets (UZFS), have been measured by THz-EPR spectroscopy, which allows to distinguish the two crystallographically independent species present in one of the complexes. Based on these experimental UZFS energies together with those for related complexes reported in literature, it was possible to establish magneto-structural correlations. UZFS linearly depends on the elongation parameter εT of the (pseudo-)tetrahedral coordination, which is given by the ratio between the average obtuse and acute angles at the cobalt(II) ion, while UZFS was found to be virtually independent of the twist angle of the chelate planes. With increasing deviation from the orthogonality of the latter, the rhombicity (|E/D|) increases.
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The flavoprotein Cytochrome P450 reductase (CPR) is the unique electron pathway from NADPH to Cytochrome P450 (CYPs). The conformational dynamics of human CPR in solution, which involves transitions from a "locked/closed" to an "unlocked/open" state, is crucial for electron transfer. To date, however, the factors guiding these changes remain unknown. By Site-Directed Spin Labelling coupled to Electron Paramagnetic Resonance spectroscopy, we have incorporated a non-canonical amino acid onto the flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) domains of soluble human CPR, and labelled it with a specific nitroxide spin probe. Taking advantage of the endogenous FMN cofactor, we successfully measured for the first time, the distance distribution by DEER between the semiquinone state FMNH⢠and the nitroxide. The DEER data revealed a salt concentration-dependent distance distribution, evidence of an "open" CPR conformation at high salt concentrations exceeding previous reports. We also conducted molecular dynamics simulations which unveiled a diverse ensemble of conformations for the "open" semiquinone state of the CPR at high salt concentration. This study unravels the conformational landscape of the one electron reduced state of CPR, which had never been studied before.
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Aminoácidos , NADPH-Ferrihemoproteína Reductasa , Óxidos de Nitrógeno , Humanos , Oxidación-Reducción , NADPH-Ferrihemoproteína Reductasa/metabolismo , Aminoácidos/metabolismo , Marcadores de Spin , Espectroscopía de Resonancia por Spin del Electrón , Transporte de Electrón , NADP/química , Flavinas/química , Compuestos Orgánicos , Mononucleótido de Flavina/química , Flavina-Adenina Dinucleótido/química , CinéticaRESUMEN
In the brains of Alzheimer's disease patients, fibrillar aggregates containing amyloid-beta (Aß) peptides are found, along with elevated concentrations of Cu(II) ions. The aggregation pathways of Aß peptides can be modulated by Cu(II) ions and is determined by the formation and nature of the Cu(II)-Aß complex. If spin-labeled, the Cu(II)-Aß complex contains two dipolar coupled paramagnetic centers, the spin label and the Cu(II) ion. Measurement of the dipolar coupling between these paramagnetic centers by relaxation-induced dipolar modulation enhancement (RIDME) allows to monitor the complex formation and thus opens a way to follow the Cu(II) transfer between peptides if a mixture of wild-type and spin-labeled ones is used. We evaluate this approach for a specific Cu(II)-Aß complex, the aggregation-inert Componentâ II. The kinetics of the Cu(II) transfer can be resolved by performing RIDME in a time-dependent manner. A temporal resolution of seconds has been achieved, with the potential to reach milliseconds, using a rapid-freeze quench device to stop the Cu(II) transfer in solution after defined incubation times.
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Péptidos beta-Amiloides , Cobre , Cobre/química , Péptidos beta-Amiloides/química , Péptidos beta-Amiloides/metabolismo , Cinética , Humanos , Espectroscopía de Resonancia por Spin del ElectrónRESUMEN
Polymeric micelles are nanocarriers for drug, protein and gene delivery due to their unique core/shell structure, which encapsulates and protects therapeutic cargos with diverse physicochemical properties. However, information regarding the micellar nanoenvironment's fluidity can provide unique insight into their makeup. In this study, we used electron paramagnetic resonance (EPR) spectroscopy to study free radical spin probe (5-doxylstearate methyl ester, 5-MDS, and 16-doxylstearic acid, 16-DS) behaviour in methoxy-poly(ethylene oxide)-poly(α-benzyl carboxylate-ε-caprolactone) (PEO-PBCL) and methoxy-poly(ethylene oxide)-poly(ε-caprolactone) (PEO-PCL) polymeric micelles. Spin probes provided information about the spectroscopic rotational correlation time (τ, s) and the spectroscopic partition parameter F. We hypothesized that spin probes would partition into the polymeric micelles, and these parameters would be calculated. The results showed that both 5-MDS and 16-DS spectra were modulated in the presence of polymeric micelles. Based on τ values, 5-MDS revealed that PEO-PCL (τ = 3.92 ± 0.26 × 10-8 s) was more fluid than PEO-PBCL (τ = 7.15 ± 0.63 × 10-8 s). The F parameter, however, could not be calculated due to the rotational hindrance of the probe within the micelles. With 16-DS, more probe rotation was observed, and although the F parameter could be calculated, it was not helpful to distinguish the micelles' fluidity. Also, doxorubicin-loading interfered with the spin probes, particularly for 16-DS. However, using simulations, we could distinguish the hydrophilic and hydrophobic components of the 16-DS probe. The findings suggest that EPR spectroscopy is a valuable method for determining core fluidity in polymeric micelles.
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Micelas , Espectroscopía de Resonancia por Spin del Electrón/métodos , Poliésteres/química , Polietilenglicoles/química , Marcadores de Spin , Polímeros/químicaRESUMEN
The radical S-adenosylmethionine (rSAM) enzyme SuiB catalyzes the formation of an unusual carbon-carbon bond between the sidechains of lysine (Lys) and tryptophan (Trp) in the biosynthesis of a ribosomal peptide natural product. Prior work on SuiB has suggested that the Lys-Trp cross-link is formed via radical electrophilic aromatic substitution (rEAS), in which an auxiliary [4Fe-4S] cluster (AuxI), bound in the SPASM domain of SuiB, carries out an essential oxidation reaction during turnover. Despite the prevalence of auxiliary clusters in over 165,000 rSAM enzymes, direct evidence for their catalytic role has not been reported. Here, we have used electron paramagnetic resonance (EPR) spectroscopy to dissect the SuiB mechanism. Our studies reveal substrate-dependent redox potential tuning of the AuxI cluster, constraining it to the oxidized [4Fe-4S]2+ state, which is active in catalysis. We further report the trapping and characterization of an unprecedented cross-linked Lys-Trp radical (Lys-Trpâ¢) in addition to the organometallic Ω intermediate, providing compelling support for the proposed rEAS mechanism. Finally, we observe oxidation of the Lys-Trp⢠intermediate by the redox-tuned [4Fe-4S]2+ AuxI cluster by EPR spectroscopy. Our findings provide direct evidence for a role of a SPASM domain auxiliary cluster and consolidate rEAS as a mechanistic paradigm for rSAM enzyme-catalyzed carbon-carbon bond-forming reactions.
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Proteínas Bacterianas/química , Proteínas Hierro-Azufre/química , Lisina/química , Proteínas Ribosómicas/química , S-Adenosilmetionina/química , Streptococcus/química , Triptófano/química , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Sitios de Unión , Catálisis , Clonación Molecular , Espectroscopía de Resonancia por Spin del Electrón , Escherichia coli/genética , Escherichia coli/metabolismo , Expresión Génica , Vectores Genéticos/química , Vectores Genéticos/metabolismo , Proteínas Hierro-Azufre/genética , Proteínas Hierro-Azufre/metabolismo , Cinética , Lisina/metabolismo , Modelos Moleculares , Oxidación-Reducción , Unión Proteica , Conformación Proteica en Hélice alfa , Conformación Proteica en Lámina beta , Dominios y Motivos de Interacción de Proteínas , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Proteínas Ribosómicas/genética , Proteínas Ribosómicas/metabolismo , S-Adenosilmetionina/metabolismo , Streptococcus/enzimología , Streptococcus/genética , Especificidad por Sustrato , Termodinámica , Triptófano/metabolismoRESUMEN
Motor control requires a coordinated ensemble of spatiotemporally precise neural oscillations across a distributed motor network, particularly in the beta range (15 to 30 Hz) to successfully plan and execute volitional actions. While substantial evidence implicates beta activity as critical to motor control, the molecular processes supporting these microcircuits and their inherent oscillatory dynamics remain poorly understood. Among these processes are mitochondrial integrity and the associated redox environments, although their direct impact on human neurophysiological function is unknown. Herein, 40 healthy adults completed a motor sequence paradigm during magnetoencephalography (MEG). MEG data were imaged in the time-frequency domain using a beamformer to evaluate beta oscillatory profiles during distinct phases of motor control (i.e., planning and execution) and subsequent behavior. To comprehensively quantify features of the mitochondrial redox environment, we used state-of-the-art systems biology approaches including Seahorse Analyzer to assess mitochondrial respiration and electron paramagnetic resonance spectroscopy to measure superoxide levels in whole blood as well as antioxidant activity assays. Using structural equation modeling, we tested the relationship between mitochondrial function and sensorimotor brain-behavior dynamics through alterations in the redox environment (e.g., generation of superoxide and alteration in antioxidant defenses). Our results indicated that superoxide-sensitive but not hydrogen peroxide-sensitive features of the redox environment had direct and mediating effects on the bioenergetic-neural pathways serving motor performance in healthy adults. Importantly, our results suggest that alterations in the redox environment may directly impact behavior above and beyond mitochondrial respiratory capacities alone and further may be effective targets for age- and disease-related declines in cognitive-motor function.
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Corteza Sensoriomotora/fisiología , Adulto , Anciano , Ritmo beta/fisiología , Femenino , Humanos , Peróxido de Hidrógeno/metabolismo , Magnetoencefalografía , Masculino , Persona de Mediana Edad , Mitocondrias/metabolismo , Modelos Neurológicos , Movimiento/fisiología , Vías Nerviosas/fisiología , Oxidación-Reducción , Desempeño Psicomotor/fisiología , Superóxidos/metabolismo , Adulto JovenRESUMEN
Oxidative stress is a major source of ROS-mediated damage to macromolecules, tissues, and the whole body. It is an important marker in the severe picture of pathological conditions. The discovery of free radicals in biological systems gives a "start" to studying various pathological processes related to the development and progression of many diseases. From this moment on, the enrichment of knowledge about the participation of free radicals and free-radical processes in the pathogenesis of cardiovascular, neurodegenerative, and endocrine diseases, inflammatory conditions, and infections, including COVID-19, is increasing exponentially. Excessive inflammatory responses and abnormal reactive oxygen species (ROS) levels may disrupt mitochondrial dynamics, increasing the risk of cell damage. In addition, low serum albumin levels and changes in the normal physiological balance between reduced and oxidized albumin can be a serious prerequisite for impaired antioxidant capacity of the body, worsening the condition in patients. This review presents the interrelationship between oxidative stress, inflammation, and low albumin levels, which are hallmarks of COVID-19.
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COVID-19 , Hipoalbuminemia , Estrés Oxidativo , SARS-CoV-2 , Humanos , COVID-19/metabolismo , Hipoalbuminemia/metabolismo , Especies Reactivas de Oxígeno/metabolismo , Biomarcadores , Óxidos de Nitrógeno/metabolismo , Inflamación/metabolismoRESUMEN
Ovalbumin (OVA), a protein vital for chick embryo nutrition, hydration, and antimicrobial protection, together with other egg-white proteins, migrates to the amniotic fluid and is orally absorbed by the embryo during embryogenesis. Recently, it has been shown that for optimal eggshell quality, the hen diet can be supplemented with manganese. Although essential for embryonic development, manganese in excess causes neurotoxicity. This study investigates whether OVA may be involved in the regulation of manganese levels. The binding of Mn(II) to OVA was investigated using electron paramagnetic resonance (EPR) spectroscopy. The results show that OVA binds a maximum of two Mn(II) ions, one with slightly weaker affinity, even in a 10-fold excess, suggesting it may have a protective role from Mn(II) overload. It seems that the binding of Mn(II), or the presence of excess Mn(II), does not affect OVA's tertiary structure, as evidenced from fluorescence and UV/vis measurements. Comparative analysis with bovine and human serum albumins revealed that they exhibit higher affinities for Mn(II) than OVA, most likely due to their essentially different physiological roles. These findings suggest that OVA does not play a role in the transport and storage of manganese; however, it may be involved in embryo protection from manganese-induced toxicity.
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Desarrollo Embrionario , Homeostasis , Manganeso , Ovalbúmina , Manganeso/metabolismo , Animales , Embrión de Pollo , Espectroscopía de Resonancia por Spin del Electrón/métodos , Humanos , Unión Proteica , Bovinos , PollosRESUMEN
Two diphosphanes with variable-length ligands tested as nucleophiles to prepare isoporphyrin copolymers in the presence of ditolylporphyrin of zinc (ZnT2P) prevented the oxidation of the diphosphine ligand. This paper demonstrates the power of this approach and describes the photoelectrocatalytic properties. The obtained copolymers were characterized by UV-vis spectroscopy, X-ray photoelectron spectroscopy, atomic force micrograph (AFM), EQCM (Electrochemical Quartz Cristal Microbalance) and electrochemistry. Their impedance properties (EIS) were studied and their photovoltaic performances were also investigated by photocurrent transient measurements under visible light irradiation.
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Chromium complexes containing a bis(diphenylphosphino) ligand have attracted significant interest over many years due to their potential as active catalysts for ethylene oligomerisation when combined with suitable co-catalysts such as triethylaluminium (TEA) or methylaluminoxane (MAO). While there has been considerable attention devoted to the possible reaction intermediates and the nature of the Cr oxidation states involved, the potential UV photoactivity of the Cr(I) complexes has so far been overlooked. Therefore, to explore the photoinduced transformations of bis(diphenylphosphino) stabilized Cr(I) complexes, we used continuous-wave (CW) EPR to study the effects of UV radiation on a cationic [Cr(CO)4(dppp)]+[Al(OC(CF3)3)4]- complex (1), where dppp represents the 1,3 bis-(diphenylphosphino)propane ligand, Ph2P(C3H6)PPh2. Our preliminary investigations into the photochemistry of this complex revealed that [Cr(CO)4(dppp)]+ (1) can be readily photo-converted into an intermediate mer-[Cr(CO)3(κ1-dppp)(κ2-dppp)]+ complex (2) and eventually into a trans-[Cr(CO)2(dppp)2]+ complex (3) in solution at room temperature under UV-A light. Here, we show that the intermediate species (2) involved in this transformation can be identified by EPR at much lower temperature (140 K) and at a specific wavelength (highlighting the wavelength dependency of the reaction). In addition, small amounts of a 'piano-stool'-type complex, namely [Cr(CO)2(dppp-η6-arene)]+ (4), can also be formed during the photoconversion of [Cr(CO)4(dppp)]+ using UV-A light. There was no evidence for the formation of the [Cr(L-bis-η6-arene)]+ complex (5) in these UV irradiation experiments. For the first time, we also evidence the formation of a 1-hexene coordinated [Cr(CO)3(dppp)(1-hexene)]+ complex (6) following UV irradiation of [Cr(CO)4(dppp)]+ in the presence of 1-hexene; this result demonstrates the unprecedented opportunity for exploiting light activation during Cr-driven olefin oligomerisation catalysis, instead of expensive, difficult-to-handle, and hazardous chemical activators.
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The cytochrome P450 family consists of ubiquitous monooxygenases with the potential to perform a wide variety of catalytic applications. Among the members of this family, CYP116B5hd shows a very prominent resistance to peracid damage, a property that makes it a promising tool for fine chemical synthesis using the peroxide shunt. In this meticulous study, we use hyperfine spectroscopy with a multifrequency approach (X- and Q-band) to characterize in detail the electronic structure of the heme iron of CYP116B5hd in the resting state, which provides structural details about its active site. The hyperfine dipole-dipole interaction between the electron and proton nuclear spins allows for the locating of two different protons from the coordinated water and a beta proton from the cysteine axial ligand of heme iron with respect to the magnetic axes centered on the iron. Additionally, since new anti-cancer therapies target the inhibition of P450s, here we use the CYP116B5hd system-imidazole as a model for studying cytochrome P450 inhibition by an azo compound. The effects of the inhibition of protein by imidazole in the active-site geometry and electron spin distribution are presented. The binding of imidazole to CYP116B5hd results in an imidazole-nitrogen axial coordination and a low-spin heme FeIII. HYSCORE experiments were used to detect the hyperfine interactions. The combined interpretation of the gyromagnetic tensor and the hyperfine and quadrupole tensors of magnetic nuclei coupled to the iron electron spin allowed us to obtain a precise picture of the active-site geometry, including the orientation of the semi-occupied orbitals and magnetic axes, which coincide with the porphyrin N-Fe-N axes. The electronic structure of the iron does not seem to be affected by imidazole binding. Two different possible coordination geometries of the axial imidazole were observed. The angles between gx (coinciding with one of the N-Fe-N axes) and the projection of the imidazole plane on the heme were determined to be -60° and -25° for each of the two possibilities via measurement of the hyperfine structure of the axially coordinated 14N.
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Compuestos Férricos , Hemo , Hemo/química , Espectroscopía de Resonancia por Spin del Electrón/métodos , Compuestos Férricos/química , Protones , Hierro/química , Imidazoles/química , Sistema Enzimático del Citocromo P-450RESUMEN
Reaction of a molecular zinc-hydride [{(ArNCMe)2CH}ZnH] (Ar = 2,6-di-isopropylphenyl) with 0.5 equiv. of [Ni(CO)Cp]2 led to the isolation of a nickel-zinc hydride complex containing a bridging 3-centre,2-electron Ni-H-Zn interaction. This species has been characterized in the solid-state by single crystal X-ray diffraction. DFT calculations are consistent with its formulation as a σ-complex derived from coordination of the zinc-hydride to a paramagnetic nickel(I) fragment. Continuous wave and pulse EPR experiments suggest that this species is not stable in solution and suggest that this species is labile in solution. Further experiments show that in the presence of catalytic quantities of nickel(I) precursors, zinc-hydride bonds can undergo either H/D-exchange with D2 or dehydrocoupling to form Zn-Zn bonds. In combination, the data support the activation and functionalisation of zinc-hydride bonds at nickel(I) centres.
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We used EPR spectroscopy to characterize the structure of RNA duplexes and their internal twist, stretch and bending motions. We prepared eight 20-base-pair-long RNA duplexes containing the rigid spin-label Çm, a cytidine analogue, at two positions and acquired orientation-selective PELDOR/DEER data. By using different frequency bands (X-, Q-, G-band), detailed information about the distance and orientation of the labels was obtained and provided insights into the global conformational dynamics of the RNA duplex. We used 19F Mims ENDOR experiments on three singly Çm- and singly fluorine-labeled RNA duplexes to determine the exact position of the Çm spin label in the helix. In a quantitative comparison to MD simulations of RNA with and without Çm spin labels, we found that state-of-the-art force fields with explicit parameterization of the spin label were able to describe the conformational ensemble present in our experiments. The MD simulations further confirmed that the Çm spin labels are excellent mimics of cytidine inducing only small local changes in the RNA structure. Çm spin labels are thus ideally suited for high-precision EPR experiments to probe the structure and, in conjunction with MD simulations, motions of RNA.
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Simulación de Dinámica Molecular , Conformación de Ácido Nucleico , ARN , Espectroscopía de Resonancia por Spin del Electrón , ARN/química , Marcadores de SpinRESUMEN
The synthesis of diradical organic compounds has garnered significant attention due to their thermally accessible spin inversion and optoelectronic properties. Yet, preparing such stable structures with high open-shell behavior remains challenging. Herein, we report the synthesis and properties of four π-extended, fused fluorene derivatives with high diradical character, taking advantage of a molecular design where the closed-shell does not include any Clar sextet, comparatively to a maximum of 5 in the corresponding open-shell state. This led to an unusual open-shell triplet ground state with an outstanding singlet-triplet energy difference (ΔEST) of ca. 19 kcal/mol, one of the highest values reported to date for an all-carbon conjugated scaffold. Incorporation of dithiafulvene units at each end of the molecule (at the five-membered rings) furnishes extended tetrathiafulvalenes (TTFs) undergoing reversible oxidations to the radical cation and diradical dication. The various pro-aromatic structures presented herein show highly localized spin density and a limited conjugation due to the confined π-electrons in the aromatic cycles, as supported by 1H NMR, UV-visible, EPR spectroscopy and DFT calculations.
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Phosphorus-centered disbiradicals, in which the radical sites exist as individual spin doublets with weak spin-spin interaction have not been known so far. Starting from monoradicals of the type [â P(µ-NTer)2 P-R], we have now succeeded in linking two such monoradical phosphorus centers by appropriate choice of a linker. To this end, biradical [â P(µ-NTer)2 Pâ ] (1) was treated with 1,6-dibromohexane, affording the brominated species {Br[P(µ-NTer)]2 }2 C6 H12 (3). Subsequent reduction with KC8 led to the formation of the disbiradical {â [P(µ-NTer)]2 }2 C6 H12 (4) featuring a large distance between the radical phosphorus sites in the solid state and formally the highest biradical character observed in a P-centered biradical so far, approaching 100 %. EPR spectroscopy revealed a three-line signal in solution with a considerably larger exchange interaction than would be expected from the molecular structure of the single crystal. Quantum chemical calculations revealed a highly dynamic conformational space; thus, the two radical sites can approach each other with a much smaller distance in solution. Further reduction of 4 resulted in the formation of a potassium salt featuring the first structurally characterized P-centered distonic radical anion (5- ). Moreover, 4 could be used in small molecule activation.