Showing papers on "Hydrogen atom abstraction published in 2020"
TL;DR: In this article, carbon based bimetallic oxides with oxygen vacancies were prepared toward peroxymonosulfate (PMS) activation for 4-aminobenzoic acid ethyl ester (ABEE) degradation.
70 citations
TL;DR: A fundamentally distinct radical generation method, as well as reaction pathways of NHC-boryl radicals enabled by photoredox catalysis, are reported, which open up new avenues for the synthesis of densely functionalized organoborons.
Abstract: Radical borylation using N-heterocyclic carbene (NHC)-BH3 complexes as boryl radical precursors has emerged as an important synthetic tool for organoboron assembly. However, the majority of reported methods are limited to reaction modes involving carbo- and/or hydroboration of specific alkenes and alkynes. Moreover, the generation of NHC-boryl radicals relies principally on hydrogen atom abstraction with the aid of radical initiators. A distinct radical generation method is reported, as well as the reaction pathways of NHC-boryl radicals enabled by photoredox catalysis. NHC-boryl radicals are generated via a single-electron oxidation and subsequently undergo cross-coupling with the in-situ-generated radical anions to yield gem-difluoroallylboronates. A photoredox-catalyzed radical arylboration reaction of alkenes was achieved using cyanoarenes as arylating components from which elaborated organoborons were accessed. Mechanistic studies verified the oxidative formation of NHC-boryl radicals through a single-electron-transfer pathway.
66 citations
TL;DR: This study finds that the excited triplet states of photosensitizers could induce a direct photosensitized oxidation of SO2 into sulfate S(VI) through energy transfer or electron transfer, and appears to be a new and ubiquitous chemical route for atmospheric sulfate production.
Abstract: Northern China is regularly subjected to intense wintertime "haze events", with high levels of fine particles that threaten millions of inhabitants. While sulfate is a known major component of these fine haze particles, its formation mechanism remains unclear especially under highly polluted conditions, with state-of-the-art air quality models unable to reproduce or predict field observations. These haze conditions are generally characterized by simultaneous high emissions of SO2 and photosensitizing materials. In this study, we find that the excited triplet states of photosensitizers could induce a direct photosensitized oxidation of hydrated SO2 and bisulfite into sulfate S(VI) through energy transfer, electron transfer, or hydrogen atom abstraction. This photosensitized pathway appears to be a new and ubiquitous chemical route for atmospheric sulfate production. Compared to other aqueous-phase sulfate formation pathways with ozone, hydrogen peroxide, nitrogen dioxide, or transition-metal ions, the results also show that this photosensitized oxidation of S(IV) could make an important contribution to aerosol sulfate formation in Asian countries, particularly in China.
57 citations
TL;DR: In this article, a new mechanism, namely radical adduct formation followed by hydrogen atom abstraction (RAF-HAA), was proposed, based on the Quantum Theory of Atoms in Molecules and Natural Bond Orbital theory.
52 citations
TL;DR: In this research, the activity of flavones and flavonols in a water solvent was studied with the density functional theory methods and hydrogen bonding, catechol moiety activity and the probability of electron density swap between rings were established.
Abstract: Flavonoids are known for their antiradical capacity, and this ability is strongly structure-dependent. In this research, the activity of flavones and flavonols in a water solvent was studied with the density functional theory methods. These included examination of flavonoids’ molecular and radical structures with natural bonding orbitals analysis, spin density analysis and frontier molecular orbitals theory. Calculations of determinants were performed: specific, for the three possible mechanisms of action—hydrogen atom transfer (HAT), electron transfer–proton transfer (ETPT) and sequential proton loss electron transfer (SPLET); and the unspecific—reorganization enthalpy (RE) and hydrogen abstraction enthalpy (HAE). Intramolecular hydrogen bonding, catechol moiety activity and the probability of electron density swap between rings were all established. Hydrogen bonding seems to be much more important than the conjugation effect, because some structures tends to form more intramolecular hydrogen bonds instead of being completely planar. The very first hydrogen abstraction mechanism in a water solvent is SPLET, and the most privileged abstraction site, indicated by HAE, can be associated with the C3 hydroxyl group of flavonols and C4’ hydroxyl group of flavones. For the catechol moiety, an intramolecular reorganization to an o-benzoquinone-like structure occurs, and the ETPT is favored as the second abstraction mechanism.
44 citations
TL;DR: The use of combined quantum mechanics/molecular mechanics and molecular dynamics simulations are described to explore the mechanism of PHF8, including dioxygen activation, 2OG binding modes, and substrate demethylation steps and demonstrate the crucial role of conformational flexibility in effective hydrogen transfer.
Abstract: PHF8 (KDM7B) is a human non-heme 2-oxoglutarate (2OG) JmjC domain oxygenase that catalyzes the demethylation of the di/mono-Ne-methylated K9 residue of histone H3. Altered PHF8 activity is linked to genetic diseases and cancer; thus, it is an interesting target for epigenetic modulation. We describe the use of combined quantum mechanics/molecular mechanics (QM/MM) and molecular dynamics (MD) simulations to explore the mechanism of PHF8, including dioxygen activation, 2OG binding modes, and substrate demethylation steps. A PHF8 crystal structure manifests the 2OG C-1 carboxylate bound to iron in a nonproductive orientation, i.e., trans to His247. A ferryl-oxo intermediate formed by activating dioxygen bound to the vacant site in this complex would be nonproductive, i.e., "off-line" with respect to reaction with Ne-methylated K9. We show rearrangement of the "off-line" ferryl-oxo intermediate to a productive "in-line" geometry via a solvent exchange reaction (called "ferryl-flip") is energetically unfavorable. The calculations imply that movement of the 2OG C-1 carboxylate prior to dioxygen binding at a five-coordination stage in catalysis proceeds with a low barrier, suggesting that two possible 2OG C-1 carboxylate geometries can coexist at room temperature. We explored alternative mechanisms for hydrogen atom transfer and show that second sphere interactions orient the Ne-methylated lysine in a conformation where hydrogen abstraction from a methyl C-H bond is energetically more favorable than hydrogen abstraction from the N-H bond of the protonated Ne-methyl group. Using multiple HAT reaction path calculations, we demonstrate the crucial role of conformational flexibility in effective hydrogen transfer. Subsequent hydroxylation occurs through a rebound mechanism, which is energetically preferred compared to desaturation, due to second sphere interactions. The overall mechanistic insights reveal the crucial role of iron-center rearrangement, second sphere interactions, and conformational flexibility in PHF8 catalysis and provide knowledge useful for the design of mechanism-based PHF8 inhibitors.
40 citations
TL;DR: Computational studies reveal that catalysis proceeds through hydrogen atom abstraction followed by radical rebound, as observed in the P450's native C-H hydroxylation mechanism, which extends Nature's impressive catalytic repertoire.
Abstract: Compared to the biological world's rich chemistry for functionalizing carbon, enzymatic transformations of the heavier homologue silicon are rare. We report that a wild-type cytochrome P450 monooxygenase (P450BM3 from Bacillus megaterium, CYP102A1) has promiscuous activity for oxidation of hydrosilanes to give silanols. Directed evolution was applied to enhance this non-native activity and create a highly efficient catalyst for selective silane oxidation under mild conditions with oxygen as the terminal oxidant. The evolved enzyme leaves C-H bonds present in the silane substrates untouched, and this biotransformation does not lead to disiloxane formation, a common problem in silanol syntheses. Computational studies reveal that catalysis proceeds through hydrogen atom abstraction followed by radical rebound, as observed in the native C-H hydroxylation mechanism of the P450 enzyme. This enzymatic silane oxidation extends nature's impressive catalytic repertoire.
37 citations
TL;DR: The generation of an organochromium-type carbanion species from a non-activated C-H bond and its nucleophilic addition to aldehydes is described and carbon radical intermediates generated by decatungstate photocatalyst-mediated hydrogen abstraction were captured by a chromium salt with the reductive radical-polar crossover reaction.
35 citations
TL;DR: The radical addition/cyclization/HAT (hydrogen atom transfer) reaction sequences of 1,6-enynes and 1-6-dienes were highly efficient delivering the desired heterocycles in good yields.
26 citations
TL;DR: A comprehensive study describing the reaction mechanism through kinetic studies, isotope labeling experiments, 19F NMR, electrochemical studies, synthetic probes, and computational experiments suggests intermolecular hydrogen atom transfer (HAT) chemistry at play, rather than classical Norrish hydrogen atom abstraction as initially conceived.
Abstract: Recently, our group reported that enone and ketone functional groups, upon photoexcitation, can direct site-selective sp3 C-H fluorination in terpenoid derivatives. How this transformation actually occurred remained mysterious, as a significant number of mechanistic possibilities came to mind. Herein, we report a comprehensive study describing the reaction mechanism through kinetic studies, isotope-labeling experiments, 19F NMR, electrochemical studies, synthetic probes, and computational experiments. To our surprise, the mechanism suggests intermolecular hydrogen atom transfer (HAT) chemistry is at play, rather than classical Norrish hydrogen atom abstraction as initially conceived. What is more, we discovered a unique role for photopromoters such as benzil and related compounds that necessitates their chemical transformation through fluorination in order to be effective. Our findings provide documentation of an unusual form of directed HAT and are of crucial importance for defining the necessary parameters for the development of future methods.
24 citations
TL;DR: Three experiments are described to elucidate how CysS uses Cbl, SAM, and a [4Fe- 4S] cluster to catalyze iterative methylation reactions: a cyclopropylcarbinyl rearrangement was used to trap the substrate radical and to estimate the rate of the radical substitution reaction involved in the methyl transfer.
Abstract: Cobalamin (Cbl)-dependent radical S-adenosylmethionine (SAM) methyltransferases catalyze methylation reactions at non-nucleophilic centers in a wide range of substrates. CysS is a Cbl-dependent radical SAM methyltransferase involved in cystobactamid biosynthesis. This enzyme catalyzes the sequential methylation of a methoxy group to form ethoxy, i-propoxy, s-butoxy, and t-butoxy groups on a p-aminobenzoate peptidyl carrier protein thioester intermediate. This biosynthetic strategy enables the host myxobacterium to biosynthesize a combinatorial antibiotic library of 25 cystobactamid analogues. In this Article, we describe three experiments to elucidate how CysS uses Cbl, SAM, and a [4Fe-4S] cluster to catalyze iterative methylation reactions: a cyclopropylcarbinyl rearrangement was used to trap the substrate radical and to estimate the rate of the radical substitution reaction involved in the methyl transfer; a bromoethoxy analogue was used to explore the active site topography; and deuterium isotope effects on the hydrogen atom abstraction by the adenosyl radical were used to investigate the kinetic significance of the hydrogen atom abstraction. On the basis of these experiments, a revised mechanism for CysS is proposed.
TL;DR: The selective photocatalytic energy-transfer-driven homolysis followed by decarboxylation generates the persistent iminyl radical and aryl radical, which would undergo an unprecedented intermolecular hydrogen atom abstraction from the alkyl substrate to provide the key C(sp3) radical.
TL;DR: It is shown that the FeIV═O complex in taurine dioxygenase (TauD), the αKG-dependent hydroxylase in which this intermediate was first characterized, also has a trigonal bipyramidal geometry but with an aspartate residue replacing the equatorial halide of the SyrB2 intermediate.
Abstract: The α-ketoglutarate (αKG)-dependent oxygenases catalyze a diverse range of chemical reactions using a common high-spin FeIV═O intermediate that, in most reactions, abstract a hydrogen atom from the substrate. Previously, the FeIV═O intermediate in the αKG-dependent halogenase SyrB2 was characterized by nuclear resonance vibrational spectroscopy (NRVS) and density functional theory (DFT) calculations, which demonstrated that it has a trigonal-pyramidal geometry with the scissile C-H bond of the substrate calculated to be perpendicular to the Fe-O bond. Here, we have used NRVS and DFT calculations to show that the FeIV═O complex in taurine dioxygenase (TauD), the αKG-dependent hydroxylase in which this intermediate was first characterized, also has a trigonal bipyramidal geometry but with an aspartate residue replacing the equatorial halide of the SyrB2 intermediate. Computational analysis of hydrogen atom abstraction by square pyramidal, trigonal bipyramidal, and six-coordinate FeIV═O complexes in two different substrate orientations (one more along [σ channel] and another more perpendicular [π channel] to the Fe-O bond) reveals similar activation barriers. Thus, both substrate approaches to all three geometries are competent in hydrogen atom abstraction. The equivalence in reactivity between the two substrate orientations arises from compensation of the promotion energy (electronic excitation within the d manifold) required to access the π channel by the significantly larger oxyl character present in the pπ orbital oriented toward the substrate, which leads to an earlier transition state along the C-H coordinate.
TL;DR: In this paper, a comprehensive model of H2 and Deuterium hydride (HD) formation on cold and warm grain surfaces and via hydrogenated polycyclic aromatic hydrocarbons in the Physico-chemical code PROtoplanetary DIsk/MOdel is presented.
Abstract: Context. Molecular hydrogen (H2 ) is the main constituent of the gas in the planet-forming disks that surround many pre-main-sequence stars. H2 can be incorporated in the atmosphere of the nascent giant planets in disks. Deuterium hydride (HD) has been detected in a few disks and can be considered the most reliable tracer of H2 , provided that its abundance throughout the disks with respect to H2 is well understood.Aims. We wish to form H2 and HD efficiently for the varied conditions encountered in protoplanetary disks: the densities vary from 104 to 1016 cm−3 ; the dust temperatures range from 5 to 1500 K, the gas temperatures go from 5 to a few 1000 Kelvin, and the ultraviolet radiation field can be 107 stronger than the standard interstellar field.Methods. We implemented a comprehensive model of H2 and HD formation on cold and warm grain surfaces and via hydrogenated polycyclic aromatic hydrocarbons in the physico-chemical code PROtoplanetary DIsk MOdel. The H2 and HD formation on dust grains can proceed via the Langmuir-Hinshelwood and Eley-Ridel mechanisms for physisorbed or chemisorbed H (D) atoms. H2 and HD also form by H (D) abstraction from hydrogenated neutral and ionised PAHs and via gas phase reactions.Results. H2 and HD are formed efficiently on dust grain surfaces from 10 to ~700 K. All the deuterium is converted into HD in UV shielded regions as soon as H2 is formed by gas-phase D abstraction reactions. The detailed model compares well with standard analytical prescriptions for H2 (HD) formation. At low temperature, H2 is formed from the encounter of two physisorbed atoms. HD molecules form on the grain surfaces and in the gas-phase. At temperatures greater than 20 K, the encounter between a weakly bound H- (or D-) atom or a gas-phase H (D) atom and a chemisorbed atom is the most efficient H2 formation route. H2 formation through hydrogenated PAHs alone is efficient above 80 K. However, the contribution of hydrogenated PAHs to the overall H2 and HD formation is relatively low if chemisorption on silicate is taken into account and if a small hydrogen abstraction cross-section is used. The H2 and HD warm grain surface network is a first step in the construction of a network of high-temperature surface reactions.
TL;DR: In this article, the authors investigated the pyrolysis of MeOCH2OMe combining imaging photoelectron photoion coincidence spectroscopy with vacuum ultraviolet (VUV) synchrotron radiation and CBS-QB3 theoretical calculations to unveil reaction paths and energetics.
TL;DR: Aromatic N-Heterocycles such as quinolines, isoquinolines and indolines are synthesized via a sodium tert-butoxide promoted oxidative dehydrogenation of the saturated heterocycles in DMSO solution that has a good functional group tolerance.
Abstract: Aromatic N-heterocycles such as quinolines, isoquinolines, and indolines are synthesized via sodium tert-butoxide-promoted oxidative dehydrogenation of the saturated heterocycles in DMSO solution. This reaction proceeds under mild reaction conditions and has a good functional group tolerance. Mechanistic studies suggest a radical pathway involving hydrogen abstraction of dimsyl radicals from the N-H bond or α-C-H of the substrates and subsequent oxidation of the nitrogen or α-aminoalkyl radicals.
TL;DR: Computational calculations imply that mononuclear iron(III)-superoxo is a sluggish oxidant of hydrogen atom abstraction reactions in UndA and will not be able to activate fatty acid residues by decarboxylation at room temperature.
Abstract: Decarboxylation of fatty acids is an important reaction in cell metabolism, but also has potential in biotechnology for the biosynthesis of hydrocarbons as biofuels. The recently discovered nonheme iron decarboxylase UndA is involved in the biosynthesis of 1-undecene from dodecanoic acid and using X-ray crystallography was assigned to be a mononuclear iron species. However, the work was contradicted by spectroscopic studies that suggested UndA to be more likely a dinuclear iron system. To resolve this controversy we decided to pursue a computational study on the reaction mechanism of fatty acid decarboxylation by UndA using iron(III)-superoxo and diiron(IV)-dioxo models. We tested several models with different protonation states of active site residues. Overall, however, the calculations imply that mononuclear iron(III)-superoxo is a sluggish oxidant of hydrogen atom abstraction reactions in UndA and will not be able to activate fatty acid residues by decarboxylation at room temperature. By contrast, a diiron-dioxo complex reacts with much lower hydrogen atom abstraction barriers and hence is a more likely oxidant in UndA.
TL;DR: Operando photoelectron photoion coincidence (PEPICO) spectroscopy is demonstrated as a pivotal technique for evidencing unprecedented mechanistic insights by isomer selective radical detection within complex hydrocarbon-functionalization reaction networks, such as those of catalyzed propane oxychlorination and oxybromination.
Abstract: Herein, we demonstrate operando photoelectron photoion coincidence (PEPICO) spectroscopy as a pivotal technique for evidencing unprecedented mechanistic insights by isomer-selective radical detection within complex hydrocarbon-functionalization reaction networks, such as those of catalyzed propane oxychlorination and oxybromination. In particular, while the oxychlorination is surface-confined, we show that in oxybromination alkane activation follows a gas-phase reaction mechanism with evolved bromine and bromine radicals, favoring 2-propyl over 1-propyl radical formation, as evidenced by isomer-selective threshold photoelectron analysis. Furthermore, we provide new mechanistic insights into the cracking and coking pathways that are observed in oxybromination. The first entails propargyl radical formation from consecutive hydrogen abstraction of propyl radicals, ultimately yielding benzene. The second originates from C-C bond cleavage in propane to ethyl and methyl radicals, which produce CH4 and C2H4, or undergo chain-growth reactions, forming C4-C6 species.
TL;DR: The formation mechanism and electronic structures of iron porphyrin nitrene intermediates, as well as the nitrene-mediated intermolecular C-H amination, have been studied by performing DFT and ab initio complete active space self-consistent field (CASSCF) calculations.
Abstract: The formation mechanism and electronic structures of iron porphyrin nitrene intermediates, as well as the nitrene-mediated intermolecular C-H amination, have been studied by performing DFT and ab initio complete active space self-consistent field (CASSCF) calculations. Compared with that of cobalt porphyrin nitrene and iron porphyrin carbene, the formation of iron porphyrin nitrene shows similar but different characteristics. The common feature is that all their formation is required to undergo the "far" or "close" complexes, but these complexes correspond to different energies relative to their respective reactants (isolated metalloporphyrins and azides), which is considered as one main reason to determine the reaction barriers. The overall free energy barrier for the formation of iron porphyrin nitrene was calculated to be 10.6 kcal/mol on a triplet-state surface, which is lower than those of cobalt porphyrin nitrene and iron porphyrin carbene. The departure of N2 from the close complexes formed by iron porphyrin and tosyl azide is nearly barrierless. For iron porphyrin nitrene, both CASSCF and unrestricted DFT calculations revealed that the triplet and open-shell singlet complexes correspond to very similar energies. The triplet nitrene complex can be described as [(por)(-OCH3)FeII═NTs]- ↔ [(por)(-OCH3)FeIII═N•-Ts]- ↔ [(por)(-OCH3)FeIV═N2-Ts]-, while the oss nitrene complex can be described as [(por)(-OCH3)FeIII-N•-Ts]-. Since the N atom bears a similar spin density as in cobalt porphyrin nitrene, the iron porphyrin nitrene exhibits similar activity in hydrogen abstraction. In addition, the intermolecular C-H amination catalyzed by iron porphyrin nitrene follows the hydrogen atom abstraction/radical recombination mechanism with a free energy barrier of 7.1 kcal/mol on the triplet-state surface. In general, the medium reactivity and easily prepared characteristic of iron porphyrin nitrene makes it a potential catalyst for C-H amination.
TL;DR: Cross-dehydrogenative C-O coupling of N-hydroxyimides with ketones, esters, and carboxylic acids was achieved employing the di-tert-butyl peroxide as a source of free radicals and a dehydrogenating agent to demonstrate the outstanding efficiency for the challenging CH-substrates.
Abstract: Cross-dehydrogenative C-O coupling of N-hydroxyimides with ketones, esters, and carboxylic acids was achieved employing the di-tert-butyl peroxide as a source of free radicals and a dehydrogenating agent. The proposed method is experimentally simple and demonstrates the outstanding efficiency for the challenging CH substrates, such as unactivated esters and carboxylic acids. It was shown that N-hydroxyphthalimide drastically affects the oxidative properties of t-BuOOt-Bu by intercepting the t-BuO• radicals with the formation of phthalimide-N-oxyl radicals, a species responsible for both hydrogen atom abstraction from the CH reagent and the selective formation of the C-O coupling product by selective radical cross-recombination. The practical applicability of the developed method was exemplified by the single-stage synthesis of commercial reagent (known as Baran aminating reagent precursor) from isobutyric acid and N-hydroxysuccinimide, whereas in the standard synthetic approach, four stages are necessary.
TL;DR: The switch in catalytic activity of CYP121 is revealed and the pH dependence catalytic study on the native substrate and the methoxy analogue further supports the mechanistic understanding that the hydrogen atom abstraction is the critical first oxidation step exerted by a heme-based oxidant during the cyclization reaction of cYY.
Abstract: CYP121 is a P450 enzyme from Mycobacterium tuberculosis that catalyzes a C-C coupling reaction between the two aromatic rings on its native substrate cyclo(l-Tyr-l-Tyr) (cYY) to form mycocyclosin, a necessary product for cell survival. Unlike the typical P450 enzymes for hydroxylation, CYP121 is believed to behave like a peroxidase and conduct radical-mediated C-C bond formation. Here, we probe whether the phenolic hydrogen of the substrate is the site of the postulated hydrogen atom abstraction for radical formation. We synthesized a singly O-methylated substrate analogue, cYF-4-OMe, and characterized its interaction with CYP121 by ultraviolet-visible and electron paramagnetic resonance spectroscopies and X-ray crystallography. We found that cYF-4-OMe can function as a substrate of CYP121 using the established assay via the peroxide shunt. Analysis of the enzymatic reaction revealed an O-demethylation of cYF-4-OMe instead of cyclization, yielding cYY and formaldehyde. A hydroxylated substrate, cYF-4-OMeOH, is expected to be the intermediate product, which was trapped and structurally characterized by X-ray crystallography. We further determined that the deformylation reaction of cYF-4-OMeOH proceeds via an alkyl-oxygen rather than aryl-oxygen bond cleavage by the 18O-labeling studies. Finally, the pH dependence catalytic study on the native substrate and the methoxy analogue further supports the mechanistic understanding that the hydrogen atom abstraction is the critical first oxidation step exerted by a heme-based oxidant during the cyclization reaction of cYY. The switch in catalytic activity reveals the power of CYP121 as a P450 enzyme and provides insight into the peroxidase-like catalytic mechanism.
TL;DR: It is shown that the reactivity of iron(iv)-imido complexes is dependent on the metal ligand system that affects the physicochemical properties of the oxidant such as the redox potential, which is the main driving force for the reaction mechanism with substrates.
Abstract: High-valent iron-nitrido intermediates have been postulated as reactive intermediates in various enzymes, including the nitrogenases and the cytochromes P450, but so far few have been trapped and characterized. As little is known about their oxidative and spectroscopic properties, we decided to create biomimetic models of iron(IV)-imido complexes and compare their structure and reactivity with analogous iron(IV)-oxo systems. In this work we report the synthesis and spectroscopic characterization of a novel [FeIV(NTs)(Bntpen)]2+ complex (Bntpen = N1-benzyl-N1,N2,N2-tris(pyridine-2-ylmethyl)ethane-1,2-diamine) and study its reactivity patterns with respect to hydrogen atom abstraction and nitrogen atom transfer reactions. The work is compared with analogous pentadentate ligand systems as well as with iron(IV)-oxo species with the same ligand features and highlights the differences in chemical properties and reactivity patterns. It is shown that the reactivity is dependent on the metal ligand system that affects the physicochemical properties of the oxidant such as the redox potential, which is the main driving force for the reaction mechanism with substrates.
TL;DR: The results show that the amide bond of acetamide is unaffected by hydrogen exposure, but the hydrogen abstraction activates this molecule to react with other species on its methyl site to extend its size or to include other functional groups as a first step to form COM under prebiotic or abiotic conditions.
Abstract: Acetamide (CH3CONH2) is the largest molecule containing an amide bond that has been detected in an interstellar medium; it is considered to be a precursor for complex organic molecules (COM). We utilized the advantages of a para-hydrogen (p-H2) quantum-solid matrix host to perform efficient reactions of hydrogen atoms with CH3CONH2. The H-abstraction reaction from the methyl group of CH3CONH2 to produce the 2-amino-2-oxoethyl radical, ˙CH2CONH2, was observed as the sole reaction channel in solid p-H2 at 3.3 K, consistent with theoretical predictions that this reaction has the smallest barrier among all possible channels. Our results show that the amide bond of acetamide is unaffected by hydrogen exposure, but the hydrogen abstraction activates this molecule to react with other species on its methyl site to extend its size or to include other functional groups as a first step to form COM under prebiotic or abiotic conditions. This previously neglected path should be considered in the astrochemical modeling. The photolysis of ˙CH2CONH2 at wavelengths 380-450 nm produces ketene; this step might provide a plausible mechanism to explain the anti-correlated abundance of ketene and acetamide in some astronomical observations.
TL;DR: Detailed insight is given into the selectivity of WelO5 through combined quantum mechanical/molecular mechanical (QM/MM) calculations for the whole catalytic cycle and provides a microscopic explanation for the experimental finding that S189A WelO 5 ceases to display any chlorination selectivity versus hydroxylation.
Abstract: The selectivity of halogenation versus hydroxylation in α-KG de-pendent halogenases is vital to their function and has been widely studied, particularly using the halogenase SyrB2 as a model. WelO5, a new member of α-KG dependent halogenases, catalyzes the chlorination of 12-epi-fischerindole U in the welwitindolinone biosynthetic pathway. Herein, we give a detailed insight into the selectivity of WelO5 through combined quantum mechanical/molecular mechanical (QM/MM) calculations for the whole catalytic cycle. O2 activation leads to a Fe(iv)[double bond, length as m-dash]O moiety which adopts an equatorial conformation (in the plane consisting of His164, chloride and Fe atom), in contrast to axial conformation (perpendicular to the plane). Key to the conformational selectivity is a serine residue (Ser189) in the equatorial plane, that brings the precursor of the Fe(iv)[double bond, length as m-dash]O intermediate (a Fe(ii)-peracid complex) to the equatorial conformation through hydrogen bonding. Hydrogen abstraction of the substrate by the equatorial Fe(iv)[double bond, length as m-dash]O leads to a five-coordinated HO-Fe(iii)-Cl complex, where the hydroxyl ligand is still equatorial and thus relatively far from the substrate radical in the axial direction compared to the chloride ligand. This smoothly explains the extremely high selectivity of chlorination in WelO5 and provides a microscopic explanation for the experimental finding that S189A WelO5 ceases to display any chlorination selectivity versus hydroxylation. Notably, although Ser189 is vital for the selectivity of the enzyme, it is not part of the substrate binding pocket. Therefore, WelO5 serves as an excellent example how chemoselectivity can be achieved in directed evolution without the tedious redesign of the substrate binding pocket.
TL;DR: In this paper, the BEP correlations for hydrogen abstraction reactions of biodiesel surrogates by H and OH radicals were theoretically investigated by using high-level orbital-based and ONIOM-based methods.
TL;DR: In this paper, the authors investigated the kinetics of 1,3-butadiene + ǫ-H reactions and its impact on combustion kinetic model predictions and derived the vibrational frequencies at the BH&HLYP/6-311++G(d,p) level.
TL;DR: It is shown that the catalytic cycle intermediates Compound I and Compound II of P450 can rapidly and successively abstract a phenolic hydrogen atom from adjacent peptide groups to give a biradical intermediate with small reaction barriers, enabling a selective aromatic cross-linking reaction.
Abstract: The cytochromes P450 are a versatile class of enzymes involved in many chemical reactions in biosystems and as such they take part in biodegradation as well as biosynthesis pathways in many organisms. These enzymes use molecular oxygen on a heme centre and often react as mono-oxygenases. Lesser known reactions catalyzed by the P450s include desaturation pathways and ring-closure reactions. In this work we study the aromatic cross-linking of glycopeptide units as, for instance, performed by the P450 isozyme OxyB as part of vancomycin biosynthesis. A series of density functional theory studies are reported on a large active site cluster model of 258 atoms containing the heme with its coordinated ligands, a representative substrate and its interacting protein residues. We show that the catalytic cycle intermediates Compound I and Compound II of P450 can rapidly and successively abstract a phenolic hydrogen atom from adjacent peptide groups to give a biradical intermediate with small reaction barriers. The latter can form the ether cross-link between the two aromatic residues, which is the rate-determining step in the reaction mechanism and involves a simultaneous proton transfer from the ipso-position to the ketone. A thermochemical analysis reveals that weak phenolic O-H bonds lead to hydrogen atom abstraction easily by Compound I and Compound II, enabling a selective aromatic cross-linking reaction.
TL;DR: In this paper, the catalytic effect of Ni-embedded graphene has been investigated for hydrazine (N2H4) decomposition reaction through Density Functional Theory (DFT) calculations with Grimme-D2 dispersion correction.
TL;DR: In this article, a three-parameter model equation has been proposed to describe the temperature variation of rate coefficient as k(CHF2CF2OCH2CF3+Cl) = 5.2exp(-580/T) in cm3 molecule−1s−1.