Driving force for oxygen-atom transfer by heme-thiolate enzymes.
Ontology highlight
ABSTRACT:
SUBMITTER: Wang X
PROVIDER: S-EPMC3900238 | biostudies-literature | 2013 Aug
REPOSITORIES: biostudies-literature
Publications
Driving force for oxygen-atom transfer by heme-thiolate enzymes.
Wang Xiaoshi X Peter Sebastian S Ullrich René R Hofrichter Martin M Groves John T JT
Angewandte Chemie (International ed. in English) 20130703 35
Similar Datasets
Project description:We report the syntheses, crystal structures, and characterization of the novel cis-dioxomolybdenum(VI) complexes [Tpm*MoVIO2Cl](MoO2Cl3) (1) and [Tpm*MoVIO2Cl](ClO4) (2), which are supported by the charge-neutral tris(3,5-dimethyl-1-pyrazolyl)methane (Tpm*) ligand. A comparison between isostructural [Tpm*MoVIO2Cl]+ and Tp*MoVIO2Cl [Tp* = hydrotris(3,5-dimethyl-1-pyrazolyl)borate] reveals the effects of one unit of overall charge difference on their spectroscopic and electrochemical properties, geometric and electronic structures, and O-atom-transfer (OAT) reactivities, providing new insight into pyranopterin molybdoenzyme OAT reactivity. Computational studies of these molecules indicate that the delocalized positive charge lowers the lowest unoccupied molecular orbital (LUMO) energy of cationic [Tpm*MoO2Cl]+ relative to Tp*MoO2Cl. Despite their virtually identical geometric structures revealed by crystal structures, the MoVI/MoV redox potential of 2 is increased by 350 mV relative to that of Tp*MoVIO2Cl. This LUMO stabilization also contributes to an increased effective electrophilicity of [Tpm*MoO2Cl]+ relative to that of Tp*MoO2Cl, resulting in a more favorable resonant interaction between the molydenum complex LUMO and the highest occupied molecular orbital (HOMO) of the PPh3 substrate. This leads to a greater thermodynamic driving force, an earlier transition state, and a lowered activation barrier for the orbitally controlled first step of the OAT reaction in the Tpm* system relative to the Tp* system. An Eyring plot analysis shows that this initial step yields an O≡MoIV-OPPh3 intermediate via an associative transition state, and the reaction is ∼500-fold faster for 2 than for Tp*MoO2Cl. The second step of the OAT reaction entails solvolysis of the O≡MoIV-OPPh3 intermediate to afford the solvent-substituted MoIV product and is 750-fold faster for the Tpm* system at -15 °C compared to the Tp* system. The observed rate enhancement for the second step is ascribed to a switch of the reaction mechanism from a dissociative pathway for the Tp* system to an alternative associative pathway for the Tpm* system. This is due to a more Lewis acidic MoIV center in the Tpm* system.
| S-EPMC6639825 | biostudies-literature
Project description:Some of the simplest and most powerful carbon-carbon bond forming strategies take advantage of readily accessible ubiquitous motifs: carbonyls and olefins. Here we report a fundamentally distinct mode of reactivity between carbonyls and olefins that differs from established acid-catalyzed carbonyl-ene, Prins, and carbonyl-olefin metathesis reaction paths. A range of epsilon, zeta-unsaturated ketones undergo Brønsted acid-catalyzed intramolecular cyclization to provide tetrahydrofluorene products via the formation of two new carbon-carbon bonds. Theoretical calculations and accompanying mechanistic studies suggest that this carbocyclization reaction proceeds through the intermediacy of a transient oxetane formed by oxygen atom transfer. The complex polycyclic frameworks in this product class appear as common substructures in organic materials, bioactive natural products, and recently developed pharmaceuticals.
| S-EPMC6983304 | biostudies-literature
Project description: Not available
| S-EPMC10992558 | biostudies-literature
Project description:Ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota are widespread in marine and terrestrial habitats, playing a major role in the global nitrogen cycle. However, their evolutionary history remains unexplored, which limits our understanding of their adaptation mechanisms. Here, our comprehensive phylogenomic tree of Thaumarchaeota supports three sequential events: origin of AOA from terrestrial non-AOA ancestors, colonization of the shallow ocean, and expansion to the deep ocean. Careful molecular dating suggests that these events coincided with the Great Oxygenation Event around 2300 million years ago (Mya), and oxygenation of the shallow and deep ocean around 800 and 635-560 Mya, respectively. The first transition was likely enabled by the gain of an aerobic pathway for energy production by ammonia oxidation and biosynthetic pathways for cobalamin and biotin that act as cofactors in aerobic metabolism. The first transition was also accompanied by the loss of dissimilatory nitrate and sulfate reduction, loss of oxygen-sensitive pyruvate oxidoreductase, which reduces pyruvate to acetyl-CoA, and loss of the Wood-Ljungdahl pathway for anaerobic carbon fixation. The second transition involved gain of a K+ transporter and of the biosynthetic pathway for ectoine, which may function as an osmoprotectant. The third transition was accompanied by the loss of the uvr system for repairing ultraviolet light-induced DNA lesions. We conclude that oxygen availability drove the terrestrial origin of AOA and their expansion to the photic and dark oceans, and that the stressors encountered during these events were partially overcome by gene acquisitions from Euryarchaeota and Bacteria, among other sources.
| S-EPMC6776046 | biostudies-literature
Project description:Many nucleic acid-protein structures have been resolved, though quantitative structure-activity relationship remains unclear in many cases. Thrombin complexes with G-quadruplex aptamers are striking examples of a lack of any correlation between affinity, interface organization, and other common parameters. Here, we tested the hypothesis that affinity of the aptamer-protein complex is determined with the capacity of the interface to dissipate energy of binding. Description and detailed analysis of 63 nucleic acid-protein structures discriminated peculiarities of high-affinity nucleic acid-protein complexes. The size of the amino acid sidechain in the interface was demonstrated to be the most significant parameter that correlates with affinity of aptamers. This observation could be explained in terms of need of efficient energy transfer from interacting residues. Application of energy dissipation theory provided an illustrative tool for estimation of efficiency of aptamer-protein complexes. These results are of great importance for a design of efficient aptamers.
| S-EPMC6480146 | biostudies-literature
Project description:Understanding the interplay between the kinetics and energetics of photophysical processes in perovskite-chromophore hybrid systems is crucial for realizing their potential in optoelectronics, photocatalysis, and light-harvesting applications. By combining steady-state optical characterizations and transient absorption spectroscopy, we have investigated the mechanism of interfacial charge transfer (CT) between colloidal CsPbBr3 nanoplatelets (NPLs) and surface-anchored perylene derivatives and have explored the possibility of controlling the CT rate by tuning the driving force. The CT driving force was tuned systematically by attaching acceptors with different electron affinities and by varying the bandgap of NPLs via thickness-controlled quantum confinement. Our data show that the charge-separated state is formed by selectively exciting either the electron donors or acceptors in the same system. Upon exciting attached acceptors, hole transfer from perylene derivatives to CsPbBr3 NPLs takes place on a picosecond time scale, showing an energetic behavior in line with the Marcus normal regime. Interestingly, such energetic behavior is absent upon exciting the electron donor, suggesting that the dominant CT mechanism is energy transfer followed by ultrafast hole transfer. Our findings not only elucidate the photophysics of perovskite-molecule systems but also provide guidelines for tailoring such hybrid systems for specific applications.
| S-EPMC10424230 | biostudies-literature
Project description:Hemin [Fe(III)-protoporphyrin IX] is known to bind tightly to single-stranded DNA and RNA molecules that fold into G-quadruplexes (GQ). Such complexes are strongly activated for oxidative catalysis. These heme•DNAzymes and ribozymes have found broad utility in bioanalytical and medicinal chemistry and have also been shown to occur within living cells. However, how a GQ is able to activate hemin is poorly understood. Herein, we report fast kinetic measurements (using stopped-flow UV-vis spectrophotometry) to identify the H2O2-generated activated heme species within a heme•DNAzyme that is active for the oxidation of a thioether substrate, dibenzothiophene (DBT). Singular value decomposition and global fitting analysis was used to analyze the kinetic data, with the results being consistent with the heme•DNAzyme's DBT oxidation being catalyzed by the initial Fe(III)heme-H2O2 complex. Such a complex has been predicted computationally to be a powerful oxidant for thioether substrates. In the heme•DNAzyme, the DNA GQ enhances both the kinetics of formation of the active intermediate as well as the oxidation step of DBT by the active intermediate. We show, using both stopped flow spectrophotometry and EPR measurements, that a classic Compound I is not observable during the catalytic cycle for thioether sulfoxidation.
| S-EPMC7913675 | biostudies-literature
Project description:The Cope rearrangement of selectively deuterated isotopomers of 1,5-dimethylsemibullvalene 2 a and 3,7-dicyano-1,5-dimethylsemibullvalene 2 b were studied in cryogenic matrices. In both semibullvalenes the Cope rearrangement is governed by heavy-atom tunneling. The driving force for the rearrangements is the small difference in the zero-point vibrational energies of the isotopomers. To evaluate the effect of the driving force on the tunneling probability in 2 a and 2 b, two different pairs of isotopomers were studied for each of the semibullvalenes. The reaction rates for the rearrangement of 2 b in cryogenic matrices were found to be smaller than the ones of 2 a under similar conditions, whereas differences in the driving force do not influence the rates. Small curvature tunneling (SCT) calculations suggest that the reduced tunneling rate of 2 b compared to that of 2 a results from a change in the shape of the potential energy barrier. The tunneling probability of the semibullvalenes strongly depends on the matrix environment; however, for 2 a in a qualitatively different way than for 2 b.
| S-EPMC7496793 | biostudies-literature
Project description:Three new diruthenium oxyanion complexes have been prepared, crystallographically characterized, and screened for their potential to photochemically unmask a reactive Ru-Ru?O intermediate. The most promising candidate, Ru2(chp)4ONO2 (4, chp = 6-chloro-2-hydroxypyridinate), displays a set of signals centered around m/z = 733 amu in its MALDI-TOF mass spectrum, consistent with the formation of the [Ru2(chp)4O](+) ([6](+)) ion. These signals shift to 735 amu in 4*, which contains an (18)O-labeled nitrate. EPR spectroscopy and headspace GC-MS analysis indicate that NO2(•) is released upon photolysis of 4, also consistent with the formation of 6. Photolysis of 4 in CH2Cl2 at room temperature in the presence of excess PPh3 yields OPPh3 in 173% yield; control experiments implicate 6, NO2(•), and free NO3(-) as the active oxidants. Notably, Ru2(chp)4Cl (3) is recovered after photolysis. Since 3 is the direct precursor to 4, the results described herein constitute the first example of a synthetic cycle for oxygen atom transfer that makes use of light to generate a putative metal oxo intermediate.
| S-EPMC5972014 | biostudies-literature
Project description:ATRP (atom transfer radical polymerization) is one of the most robust reversible deactivation radical polymerization (RDRP) systems. However, the limited oxygen tolerance of conventional ATRP impedes its practical use in an ambient atmosphere. In this work, we developed a fully oxygen-tolerant PICAR (photoinduced initiators for continuous activator regeneration) ATRP process occurring in both water and organic solvents in an open reaction vessel. Continuous regeneration of the oxidized form of the copper catalyst with sodium pyruvate through UV excitation allowed the chemical removal of oxygen from the reaction mixture while maintaining a well-controlled polymerization of N-isopropylacrylamide (NIPAM) or methyl acrylate (MA) monomers. The polymerizations of NIPAM were conducted with 250 ppm (with respect to the monomer) or lower concentrations of CuBr2 and a tris[2-(dimethylamino)ethyl]amine ligand. The polymers were synthesized to nearly quantitative monomer conversions (>99%), high molecular weights (M n > 270 000), and low dispersities (1.16 < Đ < 1.44) in less than 30 min under biologically relevant conditions. The reported method provided a well-controlled ATRP (Đ = 1.16) of MA in dimethyl sulfoxide despite oxygen diffusion from the atmosphere into the reaction system.
| S-EPMC8163335 | biostudies-literature