Search

Mineral particles capture water vapor in the atmosphere in the form of water films that are only few monolayers thick. Water films form nanoscale hydration environments that mediate a wide range of important reactions in nature and technology. This thesis explored two important phenomena that commonly occur within the confines of water films: mineralogical transformations (Topic 1) and photocatalytic decomposition of organics (Topic 2). These transformations were chiefly identified by vibrational spectroscopy, X-ray diffraction, X-ray photoelectron spectroscopy and (Transmission and Scanning) electron microscopy. Interpretations of reaction mechanisms were partially supported by chemometrics, kinetic and thermodynamic modeling, as well as molecular simulations. Mineralogical transformations (Topic 1) resolved in this thesis involved the hydroxylation (Papers I, II) and carbonation (Paper III) of periclase (MgO), and the oxidation of rhodochrosite (MnCO3) (Paper IV). Two types of MgO nanocubes with contrasting physical properties were used to resolve nucleation- and diffusion-limited hydroxylation reactions to brucite and carbonation reactions to amorphous magnesium carbonate (AMC). While nucleation-limited reactions completely transformed (8 nm) small and aggregated MgO nanocubes to brucite, the reactions became diffusion-limited in larger (32 nm) monodispersed MgO nanocubes because of brucite surface nanocoatings (Paper I). Additionally, brucite nanosheets grew under (GPa-level) crystallization pressures because of the important volumetric expansion of the reaction, which took place in a complex network of microporosity between the small and within the larger MgO nanocubes. Brucite stacking mechanisms, explored in Paper II, focused on the early stages of MgO-water interaction in water films of different thicknesses. These were suggested to involve the stacking and (epitaxial-like) growth of precursor Mg(OH)2 nanosheets in water films. Carbonation reactions explored

Phototrophic microorganisms, like cyanobacteria, are gaining attention as host organisms for biocatalytic processes with light as energy source and water as electron source. Redox enzymes, especially oxygenases, can profit from in-situ supply of co-substrates, i.e., reduction equivalents and O2, by the photosynthetic light reaction. The electron transfer downstream of PS I to heterologous electron consuming enzymes in principle can involve NADPH, NADH, and/or ferredoxin, whereas most direct and efficient transfer is desirable. Here, we use the model organism Synechocystis sp. PCC 6803 to investigate, to what extent host and/or heterologous constituents are involved in electron transfer to a heterologous Cytochrome P450 monooxygenase from Acidovorax sp. CHX100. Interestingly, in this highly active light-fueled cycloalkane hydroxylating biocatalyst, host-intrinsic enzymes were found capable of completely substituting the function of the Acidovorax ferredoxin reductase. To a certain extent (20%), this also was true for the Acidovorax ferredoxin. These results indicate the presence of a versatile set of electron carriers in cyanobacteria, enabling efficient and direct coupling of electron consuming reactions to photosynthetic water oxidation. This will both simplify and promote the use of phototrophic microorganisms for sustainable production processes.

Mineral particles capture water vapor in the atmosphere in the form of water films that are only few monolayers thick. Water films form nanoscale hydration environments that mediate a wide range of important reactions in nature and technology. This thesis explored two important phenomena that commonly occur within the confines of water films: mineralogical transformations (Topic 1) and photocatalytic decomposition of organics (Topic 2). These transformations were chiefly identified by vibrational spectroscopy, X-ray diffraction, X-ray photoelectron spectroscopy and (Transmission and Scanning) electron microscopy. Interpretations of reaction mechanisms were partially supported by chemometrics, kinetic and thermodynamic modeling, as well as molecular simulations. Mineralogical transformations (Topic 1) resolved in this thesis involved the hydroxylation (Papers I, II) and carbonation (Paper III) of periclase (MgO), and the oxidation of rhodochrosite (MnCO3) (Paper IV). Two types of MgO nanocubes with contrasting physical properties were used to resolve nucleation- and diffusion-limited hydroxylation reactions to brucite and carbonation reactions to amorphous magnesium carbonate (AMC). While nucleation-limited reactions completely transformed (8 nm) small and aggregated MgO nanocubes to brucite, the reactions became diffusion-limited in larger (32 nm) monodispersed MgO nanocubes because of brucite surface nanocoatings (Paper I). Additionally, brucite nanosheets grew under (GPa-level) crystallization pressures because of the important volumetric expansion of the reaction, which took place in a complex network of microporosity between the small and within the larger MgO nanocubes. Brucite stacking mechanisms, explored in Paper II, focused on the early stages of MgO-water interaction in water films of different thicknesses. These were suggested to involve the stacking and (epitaxial-like) growth of precursor Mg(OH)2 nanosheets in water films. Carbonation reactions explored

Mineral particles capture water vapor in the atmosphere in the form of water films that are only few monolayers thick. Water films form nanoscale hydration environments that mediate a wide range of important reactions in nature and technology. This thesis explored two important phenomena that commonly occur within the confines of water films: mineralogical transformations (Topic 1) and photocatalytic decomposition of organics (Topic 2). These transformations were chiefly identified by vibrational spectroscopy, X-ray diffraction, X-ray photoelectron spectroscopy and (Transmission and Scanning) electron microscopy. Interpretations of reaction mechanisms were partially supported by chemometrics, kinetic and thermodynamic modeling, as well as molecular simulations. Mineralogical transformations (Topic 1) resolved in this thesis involved the hydroxylation (Papers I, II) and carbonation (Paper III) of periclase (MgO), and the oxidation of rhodochrosite (MnCO3) (Paper IV). Two types of MgO nanocubes with contrasting physical properties were used to resolve nucleation- and diffusion-limited hydroxylation reactions to brucite and carbonation reactions to amorphous magnesium carbonate (AMC). While nucleation-limited reactions completely transformed (8 nm) small and aggregated MgO nanocubes to brucite, the reactions became diffusion-limited in larger (32 nm) monodispersed MgO nanocubes because of brucite surface nanocoatings (Paper I). Additionally, brucite nanosheets grew under (GPa-level) crystallization pressures because of the important volumetric expansion of the reaction, which took place in a complex network of microporosity between the small and within the larger MgO nanocubes. Brucite stacking mechanisms, explored in Paper II, focused on the early stages of MgO-water interaction in water films of different thicknesses. These were suggested to involve the stacking and (epitaxial-like) growth of precursor Mg(OH)2 nanosheets in water films. Carbonation reactions explored

Mineral particles capture water vapor in the atmosphere in the form of water films that are only few monolayers thick. Water films form nanoscale hydration environments that mediate a wide range of important reactions in nature and technology. This thesis explored two important phenomena that commonly occur within the confines of water films: mineralogical transformations (Topic 1) and photocatalytic decomposition of organics (Topic 2). These transformations were chiefly identified by vibrational spectroscopy, X-ray diffraction, X-ray photoelectron spectroscopy and (Transmission and Scanning) electron microscopy. Interpretations of reaction mechanisms were partially supported by chemometrics, kinetic and thermodynamic modeling, as well as molecular simulations. Mineralogical transformations (Topic 1) resolved in this thesis involved the hydroxylation (Papers I, II) and carbonation (Paper III) of periclase (MgO), and the oxidation of rhodochrosite (MnCO3) (Paper IV). Two types of MgO nanocubes with contrasting physical properties were used to resolve nucleation- and diffusion-limited hydroxylation reactions to brucite and carbonation reactions to amorphous magnesium carbonate (AMC). While nucleation-limited reactions completely transformed (8 nm) small and aggregated MgO nanocubes to brucite, the reactions became diffusion-limited in larger (32 nm) monodispersed MgO nanocubes because of brucite surface nanocoatings (Paper I). Additionally, brucite nanosheets grew under (GPa-level) crystallization pressures because of the important volumetric expansion of the reaction, which took place in a complex network of microporosity between the small and within the larger MgO nanocubes. Brucite stacking mechanisms, explored in Paper II, focused on the early stages of MgO-water interaction in water films of different thicknesses. These were suggested to involve the stacking and (epitaxial-like) growth of precursor Mg(OH)2 nanosheets in water films. Carbonation reactions explored

Two catecholase-like biomimetic catalysts, namely, two dinuclear copper complexes [Cu-2(L1)(OH)(H2O)(EtOH)][ClO4](2) (C1) and [Cu2Ac2O(L1)ClO4] (C2) with the 2,6-bis(4-methyl piperazin-1-yl-methyl)-4-formyl-phenoxy ligand (L1) together with the mononuclear complex Cu(ClO4)(2)(L2) (C3) containing ligand 1,2-(C5H4N-6-OCH3-2-CH=N)(2)CH2CH2 (L2), were synthesized. Their catalytic pathways were investigated and compared. The evaluation of the catalytic activity of compound C1 (and C2, C3) using the Michaelis-Menten model was represented by values of K-M = 272.93 (223.02; 1616) mu mol L-1 and V-max of 0.981 (1.617; 1.689) mu mol L-1 s(-1). The role of water content in the solvent is also discussed. The dinuclear complexes C1 and C2 were found to be more efficient catalysts than mononuclear complex C3. The mode of catalytic action was characterized via cyclic voltammetry, spectrophotometry, and UV-Vis spectroelectrochemistry. The catalytic mechanism of 3,5-di-tert butyl catechol oxidation in the presence of oxygen was proposed. The reaction circle was proved by the confirmation of the chemical reversibility of complex reduction. The advantage of the in situ spectroelectrochemical measurement enabled to control the reduction of quinone formed by the chemical reaction of catechol with oxygen in solution. At this step, the simultaneous change in the absorption spectrum indicated a change in the copper redox state of the catalyst., V této studii byly syntetizovány dva katecholáze podobné biomimetické katalyzátory, konkrétně dvoujaderné komplexy mědi [Cu-2(L1)(OH)(H2O)(EtOH)][ClO4](2) (C1) a [Cu2Ac2O(L1)ClO4] (C2) s 2,6-bis(4-methylpiperazin-1-yl-methyl)-4-formyl-fenoxy ligandem (L1), a dále také mononukleární komplex Cu(ClO4)(2)(L2) (C3) obsahující ligand 1,2-(C5H4N-6-OCH3-2-CH=N)(2)CH2CH2 (L2). Jejich katalytické dráhy byly zkoumány a porovnávány. Hodnocení katalytické aktivity sloučeniny C1 (a C2, C3) pomocí Michaelis-Mentenova modelu bylo popsáno hodnotami K-M = 272,93 (223,02; 1616) mu mol L-1 a V-max 0,981 (1,617; 1,689) mu mol L-1 s(-1). Diskutována je také role obsahu vody v rozpouštědle. Bylo zjištěno, že dvoujaderné komplexy C1 a C2 jsou účinnějšími katalyzátory než mononukleární komplex C3. Způsob katalytického působení byl charakterizován pomocí cyklické voltametrie, spektrofotometrie a UV-Vis spektroelektrochemie. Byl navržen katalytický mechanismus oxidace 3,5-di-terc-butylkatecholu v přítomnosti kyslíku. Potvrzením chemické vratnosti redukce komplexu byl prokázán reakční cyklus. In situ spektroelektrochemické měření umožnilo řídit redukci chinonu vzniklého chemickou reakcí katecholu s kyslíkem v roztoku. V tomto kroku indikovala změna absorpčního spektra zároveň i změnu redoxního stavu mědi.

Short-chain chlorinated paraffins (SCCPs) are listed as persistent organic pollutants (POPs) under the Stockholm Convention. Such substances are toxic, bioaccumulating, transported over long distances and degrade slowly in the environment. Certain bacterial strains of the Sphingomonadacea family are able to degrade POPs, such as hexachlorocyclohexanes (HCHs) and hexabromocyclododecanes (HBCDs). The haloalkane dehalogenase LinB, expressed in certain Sphingomonadacea, is able to catalyze the transformation of haloalkanes to hydroxylated compounds. Therefore, LinB is a promising candidate for conversion of SCCPs. Hence, a mixture of chlorinated tridecanes was exposed in vitro to LinB, which was obtained through heterologous expression in Escherichia coli. Liquid chromatography mass spectrometry (LC-MS) was used to analyze chlorinated tridecanes and their transformation products. A chloride-enhanced soft ionization method, which favors the formation of chloride adducts [M+Cl]- without fragmentation, was applied. Mathematical deconvolution was used to distinguish interfering mass spectra of paraffinic, mono-olefinic and di-olefinic compounds. Several mono- and di-hydroxylated products including paraffinic, mono-olefinic and di-olefinic compounds were found after LinB exposure. Mono- (rt = 5.9-6.9 min) and di-hydroxylated (rt = 3.2-4.5 min) compounds were separated from starting material (rt = 7.7-8.5 min) by reversed phase LC. Chlorination degrees of chlorinated tridecanes increased during LinB-exposure from nCl = 8.80 to 9.07, indicating a preferential transformation of lower chlorinated (Cl<9) tridecanes. Thus, LinB indeed catalyzed a dehalohydroxylation of chlorinated tridecanes, tridecenes and tridecadienes. The observed hydroxylated compounds are relevant CP transformation products whose environmental and toxicological effects should be further investigated.

Electrochemical hydroxylation of arenes by trifluoroacetic acid provides a straightforward access to aryl oxygen compounds under the mild and environmental benign reaction conditions. Harmful and pollutant stoichiometric amounts of oxidation reagents and the use of metal-catalysts can be avoided. Herein, we present a novel method for the synthesis of hydroxylated products from electron-rich arenes that was achieved by the implementation of a continuous-flow setup. The continuous nature of the process allowed to fine-tune the reactions conditions in order to prevent the decomposition of the sensitive products expanding the reaction scope beyond electron-poor and neutral arenes that were previously reported in the batch processes. Thus, synthetically valuable hydroxylated arenes were obtained in good yields with the residence time just over a minute. In order to demonstrate the reliability and the efficiency of the electrochemical flow setup, a scale up experiment was also performed.

[EN] The development of catalytic tools for the late-stage modification of amino acids within a peptide framework is a challenging task of capital importance. Herein, we report a Ru-catalyzed C(sp(2))-H hydroxylation of a collection of Tyr-containing di- and tripeptides featuring the use of a carbamate as a removable directing group and PhI(OCOCF3)(2) (PIFA) as oxidant. This air-compatible tagging technique is reliable, scalable and provides access to L-DOPA (L-3,4-dihydroxyphenylalanine) peptidomimetics in a racemization-free fashion. Density Functional Theory calculations support a Ru(II)/Ru(IV) catalytic cycle.

Brown carbon (BrC) absorbs radiation in the near-UV and visible ranges, affecting atmospheric photochemistry and radiative forcing. Our understanding on the photochemical transformation of BrC is still limited, especially when mixed with the abundant and photochemically labile inorganic salt, nitrate. Herein, we investigate the photochemical reactions of four BrC chromophores, including two methoxyphenols and two nitrophenols. Experiments were conducted in the absence and presence of different concentrations of H2O2and nitrate with lights of 254 and 313 nm. The results show that the pseudo-first-order decay rate constants (k) of these four BrC compounds at 313 nm illumination were approximately 10 times lower than those at 254 nm, demonstrating longer lifetimes of these BrC chromophores under tropospherically relevant irradiation. Photo-enhancement in the visible range was observed in most experiments, with those under 313 nm illumination lasting longer, indicating the prolonged effects of nascent and transformed BrC chromophores on radiative forcing. Methoxyphenols had higher averaged k values than nitrophenols during direct photolysis with 254 or 313 nm lights, but the k values for nitrophenols under high-nitrate (or high-H2O2) conditions approached those of methoxyphenols. The photo-enhancement in the visible range for methoxyphenols in the presence of nitrate was substantially contributed by nitro products, while that for nitrophenols was mainly contributed by hydroxylated and/or dimerized products. Our results reveal the similarity and difference between the photolysis of methoxyphenols and nitrophenols, which may help better understand the aging of different types of BrC for better model representation of their effects on radiative forcing. © 2022 American Chemical Society. All rights reserved.

[EN] The development of catalytic tools for the late-stage modification of amino acids within a peptide framework is a challenging task of capital importance. Herein, we report a Ru-catalyzed C(sp(2))-H hydroxylation of a collection of Tyr-containing di- and tripeptides featuring the use of a carbamate as a removable directing group and PhI(OCOCF3)(2) (PIFA) as oxidant. This air-compatible tagging technique is reliable, scalable and provides access to L-DOPA (L-3,4-dihydroxyphenylalanine) peptidomimetics in a racemization-free fashion. Density Functional Theory calculations support a Ru(II)/Ru(IV) catalytic cycle.

Brown carbon (BrC) absorbs radiation in the near-UV and visible ranges, affecting atmospheric photochemistry and radiative forcing. Our understanding on the photochemical transformation of BrC is still limited, especially when mixed with the abundant and photochemically labile inorganic salt, nitrate. Herein, we investigate the photochemical reactions of four BrC chromophores, including two methoxyphenols and two nitrophenols. Experiments were conducted in the absence and presence of different concentrations of H2O2and nitrate with lights of 254 and 313 nm. The results show that the pseudo-first-order decay rate constants (k) of these four BrC compounds at 313 nm illumination were approximately 10 times lower than those at 254 nm, demonstrating longer lifetimes of these BrC chromophores under tropospherically relevant irradiation. Photo-enhancement in the visible range was observed in most experiments, with those under 313 nm illumination lasting longer, indicating the prolonged effects of nascent and transformed BrC chromophores on radiative forcing. Methoxyphenols had higher averaged k values than nitrophenols during direct photolysis with 254 or 313 nm lights, but the k values for nitrophenols under high-nitrate (or high-H2O2) conditions approached those of methoxyphenols. The photo-enhancement in the visible range for methoxyphenols in the presence of nitrate was substantially contributed by nitro products, while that for nitrophenols was mainly contributed by hydroxylated and/or dimerized products. Our results reveal the similarity and difference between the photolysis of methoxyphenols and nitrophenols, which may help better understand the aging of different types of BrC for better model representation of their effects on radiative forcing. © 2022 American Chemical Society. All rights reserved.

Direct hydroxylation via the functionalization of tertiary benzylic C(sp(3))-H bonds is of great significance for obtaining tertiary alcohols, which find wide applications in pharmaceuticals as well as in fine chemical industries. However, current synthetic procedures use toxic reagents, and therefore, the development of a sustainable strategy for the synthesis of tertiary benzylic alcohols is highly desirable. To solve this problem, herein, we report a metal-free heterogeneous photocatalyst to synthesize the hydroxylated products using oxygen as the key reagent. Various benzylic substrates were employed into our mild reaction conditions to afford the desirable products in good to excellent yields. More importantly, the gram-scale reaction was achieved via harvesting direct solar energy and exhibited high quantity of the product. The high stability of the catalyst was proved via recycling the catalyst and spectroscopic analyses. Finally, a possible mechanism was proposed based on electron paramagnetic resonance and other experimental evidence.

Water adsorption on transition metal dichalcogenides and other 2D materials is generally governed by weak van der Waals interactions. This results in a hydrophobic character of the basal planes, and defects may play a significant role in water adsorption and water cluster nucleation. However, there is a lack of detailed experimental investigations on water adsorption on defective 2D materials. Here, by combining low-temperature scanning tunneling microscopy (STM) experiments and density functional theory (DFT) calculations, we study in that context the well-defined mirror twin boundary (MTB) networks separating mirror-grains in 2D MoSe2. These MTBs are dangling bond-free extended crystal modifications with metallic electronic states embedded in the 2D semiconducting matrix of MoSe2. Our DFT calculations indicate that molecular water also interacts similarly weak with these MTBs as with the defect-free basal plane of MoSe2. However, in low temperature STM experiments, nanoscopic water structures are observed that selectively decorate the MTB network. This localized adsorption of water is facilitated by functionalization of the MTBs by hydroxyls formed by dissociated water. Hydroxyls may form by dissociating of water at undercoordinated defects or adsorbing of radicals from the gas phase in the UHV chamber. Our DFT analysis indicates that the metallic MTBs adsorb these radicals much stronger than on the basal plane due to charge transfer from the metallic states into the molecular orbitals of the OH groups. Once the MTBs are functionalized with hydroxyls, molecular water can attach to them, forming water channels along the MTBs. This study demonstrates the role metallic defect states play in the adsorption of water even in the absence of unsaturated bonds that have been so far considered to be crucial for adsorption of hydroxyls or water.

Water adsorption on transition metal dichalcogenides and other 2D materials is generally governed by weak van der Waals interactions. This results in a hydrophobic character of the basal planes, and defects may play a significant role in water adsorption and water cluster nucleation. However, there is a lack of detailed experimental investigations on water adsorption on defective 2D materials. Here, by combining low-temperature scanning tunneling microscopy (STM) experiments and density functional theory (DFT) calculations, we study in that context the well-defined mirror twin boundary (MTB) networks separating mirror-grains in 2D MoSe2. These MTBs are dangling bond-free extended crystal modifications with metallic electronic states embedded in the 2D semiconducting matrix of MoSe2. Our DFT calculations indicate that molecular water also interacts similarly weak with these MTBs as with the defect-free basal plane of MoSe2. However, in low temperature STM experiments, nanoscopic water structures are observed that selectively decorate the MTB network. This localized adsorption of water is facilitated by functionalization of the MTBs by hydroxyls formed by dissociated water. Hydroxyls may form by dissociating of water at undercoordinated defects or adsorbing of radicals from the gas phase in the UHV chamber. Our DFT analysis indicates that the metallic MTBs adsorb these radicals much stronger than on the basal plane due to charge transfer from the metallic states into the molecular orbitals of the OH groups. Once the MTBs are functionalized with hydroxyls, molecular water can attach to them, forming water channels along the MTBs. This study demonstrates the role metallic defect states play in the adsorption of water even in the absence of unsaturated bonds that have been so far considered to be crucial for adsorption of hydroxyls or water.

Collagen is the most abundant protein in humans. It has a characteristic triple-helix structure and is heavily posttranslationally modified. The complex biosynthesis of collagen involves processing by many enzymes and chaperones in the rough endoplasmic reticulum. Lysyl hydroxylase 1 (LH1) is required to hydroxylate lysine for cross-linking and carbohydrate attachment within collagen triple helical sequences. Additionally, a recent study of prolyl 3-hydroxylase 3 (P3H3) demonstrated that this enzyme may be critical for LH1 activity; however, the details surrounding its involvement remain unclear. If P3H3 is an LH1 chaperone that is critical for LH1 activity, P3H3 and LH1 null mice should display a similar deficiency in lysyl hydroxylation. To test this hypothesis, we compared the amount and location of hydroxylysine in the triple helical domains of type V and I collagen from P3H3 null, LH1 null, and wild-type mice. The amount of hydroxylysine in type V collagen was reduced in P3H3 null mice, but surprisingly type V collagen from LH1 null mice contained as much hydroxylysine as type V collagen from wild-type mice. In type I collagen, our results indicate that LH1 plays a global enzymatic role in lysyl hydroxylation. P3H3 is also involved in lysyl hydroxylation, particularly at cross-link formation sites, but is not required for all lysyl hydroxylation sites. In summary, our study suggests that LH1 and P3H3 likely have two distinct mechanisms to recognize different collagen types and to distinguish cross-link formation sites from other sites in type I collagen.

Viral pathogens are an ongoing threat to public health worldwide. Analysing their dependence on host biosynthetic pathways could lead to effective antiviral therapies1. Here we integrate proteomic analyses of polysomes with functional genomics and pharmacological interventions to define how enteroviruses and flaviviruses remodel host polysomes to synthesize viral proteins and disable host protein production. We find that infection with polio, dengue or Zika virus markedly modifies polysome composition, without major changes to core ribosome stoichiometry. These viruses use different strategies to evict a common set of translation initiation and RNA surveillance factors from polysomes while recruiting host machineries that are specifically required for viral biogenesis. Targeting these specialized viral polysomes could provide a new approach for antiviral interventions. For example, we find that both Zika and dengue use the collagen proline hydroxylation machinery to mediate cotranslational modification of conserved proline residues in the viral polyprotein. Genetic or pharmacological inhibition of proline hydroxylation impairs nascent viral polyprotein folding and induces its aggregation and degradation. Notably, such interventions prevent viral polysome remodelling and lower virus production. Our findings delineate the modular nature of polysome specialization at the virus-host interface and establish a powerful strategy to identify targets for selective antiviral interventions.

The pilot-scale production of the peroxygenase from Agrocybe aegerita (rAaeUPO) is demonstrated. In a fed-batch fermentation of the recombinant Pichia pastoris, the enzyme was secreted into the culture medium to a final concentration of 0.29 g L-1 corresponding to 735 g of the peroxygenase in 2500 L of the fermentation broth after 6 days. Due to nonoptimized downstream processing, only 170 g of the enzyme has been isolated. The preparative usefulness of the so-obtained enzyme preparation has been demonstrated at a semipreparative scale (100 mL) as an example of the stereoselective hydroxylation of ethyl benzene. Using an adjusted H2O2 feed rate, linear product formation was observed for 7 days, producing more than 5 g L-1 (R)-1-phenyl ethanol. The biocatalyst performed more than 340.000 catalytic turnovers (942 g of the product per gram of rAaeUPO)., BT/Biocatalysis

Flavoprotein monooxygenases (FPMOs) are single- or two-component enzymes that catalyze a diverse set of chemo-, regio- and enantioselective oxyfunctionalization reactions. In this review, we describe how FPMOs have evolved from model enzymes in mechanistic flavoprotein research to biotechnologically relevant catalysts that can be applied for the sustainable production of valuable chemicals. After a historical account of the development of the FPMO field, we explain the FPMO classification system, which is primarily based on protein structural properties and electron donor specificities. We then summarize the most appealing reactions catalyzed by each group with a focus on the different types of oxygenation chemistries. Wherever relevant, we report engineering strategies that have been used to improve the robustness and applicability of FPMOs., BT/Biocatalysis

Thymol and carvacrol are phenolic monoterpenes found in thyme, oregano, and several other species of the Lamiaceae. Long valued for their smell and taste, these substances also have antibacterial and anti-spasmolytic properties. They are also suggested to be precursors of thymohydroquinone and thymoquinone, monoterpenes with anti-inflammatory, antioxidant, and antitumor activities. Thymol and carvacrol biosynthesis has been proposed to proceed by the cyclization of geranyl diphosphate to gamma-terpinene, followed by a series of oxidations via p-cymene. Here, we show that gamma-terpinene is oxidized by cytochrome P450 monooxygenases (P450s) of the CYP71D subfamily to produce unstable cyclohexadienol intermediates, which are then dehydrogenated by a short-chain dehydrogenase/reductase (SDR) to the corresponding ketones. The subsequent formation of the aromatic compounds occurs via keto-enol tautomerisms. Combining these enzymes with gamma-terpinene in in vitro assays or in vivo in Nicotiana ben-thamiana yielded thymol and carvacrol as products. In the absence of the SDRs, only p-cymene was formed by rearrangement of the cyclohexadienol intermediates. The nature of these unstable intermediates was inferred from reactions with the gamma-terpinene isomer limonene and by analogy to reactions catalyzed by related enzymes. We also identified and characterized two P450s of the CYP76S and CYP736A subfamilies that catalyze the hydroxylation of thymol and carvacrol to thymohydroquinone when heterologously expressed in yeast and N. benthamiana. Our findings alter previous views of thymol and carvacrol formation, identify the enzymes involved in the biosynthesis of these phenolic monoterpenes and thymohydroquinone in the Lamiaceae, and provide targets for metabolic engineering of high-value terpenes in plants.

Anomalous microwave emission (AME) is detected in many astrophysical environments as a foreground feature typically peaking between 20-30 GHz and extending over a 10-60 GHz range. One of the leading candidates for the source of AME is small spinning dust grains. Such grains should be very small (approx. ≤1 nm diameter) in order for the rotational emission to fall within the observed frequency range. In addition, these nanosized grains should possess a significant dipole moment to account for the observed emissivities. These constraints have been shown to be compatible with spinning bare nanosilicate clusters, assuming that ∼1% of the total Si mass budget is held in these ultrasmall grains. Silicate dust can be hydroxylated by processing in the interstellar medium and is generally known to provide seeds for molecular water ice nucleation in denser regions. Herein, we use quantum chemical calculations to investigate how the dipole moment of Mg-rich pyroxenic (MgSiO3) nanoclusters is affected by both accretion of molecular water and dissociative hydration. Our work thus provides an indication of how the formation of water ice mantles is likely to affect the capacity of nanosilicates to generate AME.

Thymol and carvacrol are phenolic monoterpenes found in thyme, oregano, and several other species of the Lamiaceae. Long valued for their smell and taste, these substances also have antibacterial and anti-spasmolytic properties. They are also suggested to be precursors of thymohydroquinone and thymoquinone, monoterpenes with anti-inflammatory, antioxidant, and antitumor activities. Thymol and carvacrol biosynthesis has been proposed to proceed by the cyclization of geranyl diphosphate to gamma-terpinene, followed by a series of oxidations via p-cymene. Here, we show that gamma-terpinene is oxidized by cytochrome P450 monooxygenases (P450s) of the CYP71D subfamily to produce unstable cyclohexadienol intermediates, which are then dehydrogenated by a short-chain dehydrogenase/reductase (SDR) to the corresponding ketones. The subsequent formation of the aromatic compounds occurs via keto-enol tautomerisms. Combining these enzymes with gamma-terpinene in in vitro assays or in vivo in Nicotiana ben-thamiana yielded thymol and carvacrol as products. In the absence of the SDRs, only p-cymene was formed by rearrangement of the cyclohexadienol intermediates. The nature of these unstable intermediates was inferred from reactions with the gamma-terpinene isomer limonene and by analogy to reactions catalyzed by related enzymes. We also identified and characterized two P450s of the CYP76S and CYP736A subfamilies that catalyze the hydroxylation of thymol and carvacrol to thymohydroquinone when heterologously expressed in yeast and N. benthamiana. Our findings alter previous views of thymol and carvacrol formation, identify the enzymes involved in the biosynthesis of these phenolic monoterpenes and thymohydroquinone in the Lamiaceae, and provide targets for metabolic engineering of high-value terpenes in plants.

The pilot-scale production of the peroxygenase from Agrocybe aegerita (rAaeUPO) is demonstrated. In a fed-batch fermentation of the recombinant Pichia pastoris, the enzyme was secreted into the culture medium to a final concentration of 0.29 g L-1 corresponding to 735 g of the peroxygenase in 2500 L of the fermentation broth after 6 days. Due to nonoptimized downstream processing, only 170 g of the enzyme has been isolated. The preparative usefulness of the so-obtained enzyme preparation has been demonstrated at a semipreparative scale (100 mL) as an example of the stereoselective hydroxylation of ethyl benzene. Using an adjusted H2O2 feed rate, linear product formation was observed for 7 days, producing more than 5 g L-1 (R)-1-phenyl ethanol. The biocatalyst performed more than 340.000 catalytic turnovers (942 g of the product per gram of rAaeUPO)., BT/Biocatalysis

Flavoprotein monooxygenases (FPMOs) are single- or two-component enzymes that catalyze a diverse set of chemo-, regio- and enantioselective oxyfunctionalization reactions. In this review, we describe how FPMOs have evolved from model enzymes in mechanistic flavoprotein research to biotechnologically relevant catalysts that can be applied for the sustainable production of valuable chemicals. After a historical account of the development of the FPMO field, we explain the FPMO classification system, which is primarily based on protein structural properties and electron donor specificities. We then summarize the most appealing reactions catalyzed by each group with a focus on the different types of oxygenation chemistries. Wherever relevant, we report engineering strategies that have been used to improve the robustness and applicability of FPMOs., BT/Biocatalysis

MXenes, an emerging family of two-dimensional (2D) metal carbides and nitrides, have been demonstrated to be effective nitrogen reduction reaction (NRR) catalysts. So far, most of the theoretical studies toward NRR are based on bare MXenes; however, the structural stabilities are questionable. In this work, we studied the NRR process on several synthesized MXenes (Ti2C, V2C, Cr2C, Zr2C, Nb2C, Mo2C, Hf2C, and Ta2C) with hydroxyl (OH) termination since the structures are preferred under NRR operating conditions as per Pourbaix stability diagrams. It is found that OH plays an essential role in tuning the NRR chemistry, as a new surface-hydroxylation mechanism. Different from the widely accepted NRR mechanism where only protons are involved in the reaction, hydrogen (H) atoms from surface hydroxyl could be captured by the intermediate and participate into the NRR, while the remaining H vacancy can subsequently be self-repaired by the protons under the applied potential. The cooperative effect of surface hydroxylation can effectively boost the NRR, while Mo2C(OH)2 stands out with the most favorable limiting potential of -0.62 V and highest selectivity. Moreover, new scaling relationships based on the H vacancy energy are established, elucidating the possibility for structure-activity tuning. This study not only elaborates the essential role of surface OH functionalization in evaluating NRR performance but also affords new insights into advance sustainable NH3 production.

Flavoprotein monooxygenases (FPMOs) are single- or two-component enzymes that catalyze a diverse set of chemo-, regio- and enantioselective oxyfunctionalization reactions. In this review, we describe how FPMOs have evolved from model enzymes in mechanistic flavoprotein research to biotechnologically relevant catalysts that can be applied for the sustainable production of valuable chemicals. After a historical account of the development of the FPMO field, we explain the FPMO classification system, which is primarily based on protein structural properties and electron donor specificities. We then summarize the most appealing reactions catalyzed by each group with a focus on the different types of oxygenation chemistries. Wherever relevant, we report engineering strategies that have been used to improve the robustness and applicability of FPMOs.

Selective oxyfunctionalizations of aliphatic compounds are difficult chemical reactions, where enzymes can play an important role due to their stereo- and regio-selectivity and operation under mild reaction conditions. P450 monooxygenases are well-known biocatalysts that mediate oxyfunctionalization reactions in different living organisms (from bacteria to humans). Unspecific peroxygenases (UPOs), discovered in fungi, have arisen as “dream biocatalysts” of great biotechnological interest because they catalyze the oxyfunctionalization of aliphatic and aromatic compounds, avoiding the necessity of expensive cofactors and regeneration systems, and only depending on H2O2 for their catalysis. Here, we summarize recent advances in aliphatic oxyfunctionalization reactions by UPOs, as well as the molecular determinants of the enzyme structures responsible for their activities, emphasizing the differences found between well-known P450s and the novel fungal peroxygenases. © 2021 The Authors

The edible filamentous fungi are hot candidate for future supply of functional food and feed with e.g. protein, essential amino acids, and compounds with immunostimulant activity. L-carnitine that plays a crucial role in energy metabolism represents a functional compound normally produced by Zygomycetes filamentous fungus Rhizopus oligosporus in solid-state fermentation. The present study provides the first insights on production of L-carnitine-enriched edible fungal biomass through submerged cultivation of several Ascomycetes and Zygomycetes including Aspergillus oryzae, Neurospora intermedia, Rhizopus oryzae, and Rhizopus oligosporus. A. oryzae with 3 mg L-carnitine yield per gram of fungal biomass, indicates great potential on production of this bioactive compound which is remarkably higher than the other tested fungi in this work and also previous studies. In addition to fungal strain, other factors such as cultivation time and presence of yeast extract were found to play a role. Further studies on submerged growth optimization of A. oryzae in both high-quality recipes and in medium based on low-value substrates are proposed in order to clarify its potential for production of L-carnitine-enriched fungal biomass.

The edible filamentous fungi are hot candidate for future supply of functional food and feed with e.g. protein, essential amino acids, and compounds with immunostimulant activity. L-carnitine that plays a crucial role in energy metabolism represents a functional compound normally produced by Zygomycetes filamentous fungus Rhizopus oligosporus in solid-state fermentation. The present study provides the first insights on production of L-carnitine-enriched edible fungal biomass through submerged cultivation of several Ascomycetes and Zygomycetes including Aspergillus oryzae, Neurospora intermedia, Rhizopus oryzae, and Rhizopus oligosporus. A. oryzae with 3 mg L-carnitine yield per gram of fungal biomass, indicates great potential on production of this bioactive compound which is remarkably higher than the other tested fungi in this work and also previous studies. In addition to fungal strain, other factors such as cultivation time and presence of yeast extract were found to play a role. Further studies on submerged growth optimization of A. oryzae in both high-quality recipes and in medium based on low-value substrates are proposed in order to clarify its potential for production of L-carnitine-enriched fungal biomass.

mTORC1 is an important regulator of muscle mass but how it is modulated by oxygen and nutrients is not completely understood. We show that loss of the prolyl hydroxylase domain isoform 1 oxygen sensor in mice (PHD1KO) reduces muscle mass. PHD1KO muscles show impaired mTORC1 activation in response to leucine whereas mTORC1 activation by growth factors or eccentric contractions was preserved. The ability of PHD1 to promote mTORC1 activity is independent of its hydroxylation activity but is caused by decreased protein content of the leucyl tRNA synthetase (LRS) leucine sensor. Mechanistically, PHD1 interacts with and stabilizes LRS. This interaction is promoted during oxygen and amino acid depletion and protects LRS from degradation. Finally, elderly subjects have lower PHD1 levels and LRS activity in muscle from aged versus young human subjects. In conclusion, PHD1 ensures an optimal mTORC1 response to leucine after episodes of metabolic scarcity.

Oxidative reactions often require unstable and environmentally harmful oxidants; therefore, the investigation of safer alternatives is urgent. Here, the hydroxylation of aryl boronic acid in the presence of Co-complexes is demonstrated. Tetrakis(4-carboxyphenyl) Co(II)-porphyrin was combined with biodegradable polymers such as chitosan catalyzed hydroxylation of phenyl boronic acids to form phenol derivatives under blue-light irradiation. This catalytic system can be used as an eco-friendly oxidation process that does not release oxidizing agents into the atmosphere., Catalysts, 10(11), art.no.1262; 2020

Exposures to persistent organohalogen chemicals during pregnancy are associated with adverse health effects. Low-income, minority women with pre-existing co-morbidities may be particularly vulnerable to these exposures, but have historically been understudied. We aimed to characterize exposures to multiple chemical classes among a sample of ethnically diverse, lower income, overweight or obese pregnant women. Serum concentrations of polybrominated diphenyl ethers (PBDEs) and their hydroxylated metabolites (OH-PBDEs), polychlorinated biphenyls (PCBs), and poly- and perfluoroalkyl substances (PFASs) were measured in 98 pregnant women (California; 2011-2013). Aggregate exposures were evaluated using correlational clustering, a "chemical burden" score, and PCA. Associations between sociodemographic characteristics and individual and aggregate exposures were evaluated using multivariable linear regression. Clustering and PCA both produced four groupings: (PC1) PBDEs/OH-PBDEs, (PC2) PCBs, (PC3) PFNA/PFOA/PFDeA, (PC4) PFHxS/PFOS. Race/ethnicity and prepregnancy BMI were associated with PBDEs, OH-PBDEs and PC1. Maternal age was associated with PCBs and PC2. Parity was associated with PBDEs, OH-PBDEs and PC2. Poverty was negatively associated with PCBs, whereas food insecurity was positively associated with PFOS. We observed variations in sociodemographic profiles of exposures by chemical class and weak across-class correlations. These findings have implications for epidemiologic studies of chemical mixtures and for exposure reduction strategies.

Sphingolipids constitute a heterogeneous lipid category that is involved in many key cellular functions. For high-throughput analyses of sphingolipids, tandem mass spectrometry (MS/MS) is the method of choice, offering sufficient sensitivity, structural information, and quantitative precision for detecting hundreds to thousands of species simultaneously. While glycerolipids and phospholipids are predominantly non-hydroxylated, sphingolipids are typically dihydroxylated. However, species containing one or three hydroxylation sites can be detected frequently. This variability in the number of hydroxylation sites on the sphingolipid long-chain base and the fatty acyl moiety produces many more isobaric species and fragments than for other lipid categories. Due to this complexity, the automated annotation of sphingolipid species is challenging, and incorrect annotations are common. In this study, we present an extension of the Lipid Data Analyzer (LDA) "decision rule set" concept that considers the structural characteristics that are specific for this lipid category. To address the challenges inherent to automated annotation of sphingolipid structures from MS/MS data, we first developed decision rule sets using spectra from authentic standards and then tested the applicability on biological samples including murine brain and human plasma. A benchmark test based on the murine brain samples revealed a highly improved annotation quality as measured by sensitivity and reliability. The results of this benchmark test combined with the easy extensibility of the software to other (sphingo)lipid classes and the capability to detect and correctly annotate novel sphingolipid species make LDA broadly applicable to automated sphingolipid analysis, especially in high-throughput settings.

The use of neat reaction media, that is the avoidance of additional solvents, is the simplest and the most efficient approach to follow in biocatalysis. Here, we show that unspecific peroxygenase from Agrocybe aegerita (AaeUPO) can hydroxylate the neat model substrate cyclohexane. H2O2 was photocatalytically generated in situ by nitrogen-doped carbon nanodots (N−CNDs) and UV LED illumination. AaeUPO entrapment in alginate beads increased enzyme stability and facilitated the reaction in neat cyclohexane. N−CNDs absorption in beads containing AaeUPO created a 2-in-1 heterogeneous photobiocatalyst that was active for up to seven days under reaction conditions and produced cyclohexanol, 2.5 mM. To increase productivity, the bead size and the photocatalyst-to-enzyme ratio have been identified as promising targets for optimisation., Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public., BT/Biocatalysis

Unspecific peroxygenases have recently gained significant interest due to their ability to catalyse the hydroxylation of non-activated C−H bonds using only hydrogen peroxide as a co-substrate. However, the development of preparative processes has so far mostly concentrated on benzylic hydroxylations using liquid substrates. Herein, we demonstrate the application of a peroxygenase for the hydroxylation of the inert, gaseous substrate butane to 2-butanol in a bubble column reactor. The influence of hydrogen peroxide feed rate and enzyme loading on product formation, overoxidation to butanone and catalytic efficiency is investigated at 200 mL scale. The process is scaled up to 2 L and coupled with continuous extraction. This setup allowed the production of 115 mmol 2-butanol and 70 mmol butanone with an overall total turnover number (TTN) of over 15.000, thereby demonstrating the applicability of peroxygenases for preparative hydroxylation of such inert, gaseous substrates at mild reaction conditions., BT/Biocatalysis

Peroxyzymes simply use H2O2 as a cosubstrate to oxidize a broad range of inert C-H bonds. The lability of many peroxyzymes against H2O2 can be addressed by a controlled supply of H2O2, ideally in situ. Here, we report a simple, robust, and water-soluble anthraquinone sulfonate (SAS) as a promising organophotocatalyst to drive both haloperoxidase-catalyzed halogenation and peroxygenase-catalyzed oxyfunctionalization reactions. Simple alcohols, methanol in particular, can be used both as a cosolvent and an electron donor for H2O2 generation. Very promising turnover numbers for the biocatalysts of up to 318 »000 have been achieved., BT/Biocatalysis

Over the last decade environmental agencies worldwide have escalated their work to phase out animal testing for the purposes of chemical regulation. Meanwhile the number of commercially available chemicals and the requirements for hazard assessments have both increased, creating a large need for substitution of traditional in vivo assays with in vitro tests. One example of this is the replacement of the OECD acute toxicity test of adult fish (test guideline [TG] 203) with zebrafish embryos (TG 236). With new insights into the toxicological properties of chemicals, the demand on these replacement tests is also changing character with a shifted focus towards mechanistic understanding of toxicity. The omics sciences encompass a group of analytical methods which have proven to be very powerful for unveiling of mechanistic information of biochemical processes. Metabolomics is one of the younger members of this family and entails the large-scale analysis of endogenous metabolites and their perturbation in living organisms. The overall objective of this thesis was to develop modifications to the TG236 OECD assay to obtain omic data suitable for use in chemical hazard assessment. To achieve this goal, we started by developing a targeted and non-targeted metabolomics workflow and evaluated the performance of the two types of analysis (Paper I). We also evaluated the efficiency of three signal drift correction approaches, which is an important step in data quality improvement for non-targeted analysis, and reported previously unlisted biochemicals present in NIST reference material. In Paper II we applied the workflow in Paper I to a newly developed, in-plate extraction method for single zebrafish embryos which were exposed to the pharmaceutical and environmental pollutant propranolol. Data processing workflows were developed to overcome challenges arising from the occurrence of the exposure compound and its biotransformation products (or in-source fragments of these) in the

Over the last decade environmental agencies worldwide have escalated their work to phase out animal testing for the purposes of chemical regulation. Meanwhile the number of commercially available chemicals and the requirements for hazard assessments have both increased, creating a large need for substitution of traditional in vivo assays with in vitro tests. One example of this is the replacement of the OECD acute toxicity test of adult fish (test guideline [TG] 203) with zebrafish embryos (TG 236). With new insights into the toxicological properties of chemicals, the demand on these replacement tests is also changing character with a shifted focus towards mechanistic understanding of toxicity. The omics sciences encompass a group of analytical methods which have proven to be very powerful for unveiling of mechanistic information of biochemical processes. Metabolomics is one of the younger members of this family and entails the large-scale analysis of endogenous metabolites and their perturbation in living organisms. The overall objective of this thesis was to develop modifications to the TG236 OECD assay to obtain omic data suitable for use in chemical hazard assessment. To achieve this goal, we started by developing a targeted and non-targeted metabolomics workflow and evaluated the performance of the two types of analysis (Paper I). We also evaluated the efficiency of three signal drift correction approaches, which is an important step in data quality improvement for non-targeted analysis, and reported previously unlisted biochemicals present in NIST reference material. In Paper II we applied the workflow in Paper I to a newly developed, in-plate extraction method for single zebrafish embryos which were exposed to the pharmaceutical and environmental pollutant propranolol. Data processing workflows were developed to overcome challenges arising from the occurrence of the exposure compound and its biotransformation products (or in-source fragments of these) in the

Over the last decade environmental agencies worldwide have escalated their work to phase out animal testing for the purposes of chemical regulation. Meanwhile the number of commercially available chemicals and the requirements for hazard assessments have both increased, creating a large need for substitution of traditional in vivo assays with in vitro tests. One example of this is the replacement of the OECD acute toxicity test of adult fish (test guideline [TG] 203) with zebrafish embryos (TG 236). With new insights into the toxicological properties of chemicals, the demand on these replacement tests is also changing character with a shifted focus towards mechanistic understanding of toxicity. The omics sciences encompass a group of analytical methods which have proven to be very powerful for unveiling of mechanistic information of biochemical processes. Metabolomics is one of the younger members of this family and entails the large-scale analysis of endogenous metabolites and their perturbation in living organisms. The overall objective of this thesis was to develop modifications to the TG236 OECD assay to obtain omic data suitable for use in chemical hazard assessment. To achieve this goal, we started by developing a targeted and non-targeted metabolomics workflow and evaluated the performance of the two types of analysis (Paper I). We also evaluated the efficiency of three signal drift correction approaches, which is an important step in data quality improvement for non-targeted analysis, and reported previously unlisted biochemicals present in NIST reference material. In Paper II we applied the workflow in Paper I to a newly developed, in-plate extraction method for single zebrafish embryos which were exposed to the pharmaceutical and environmental pollutant propranolol. Data processing workflows were developed to overcome challenges arising from the occurrence of the exposure compound and its biotransformation products (or in-source fragments of these) in the

Over the last decade environmental agencies worldwide have escalated their work to phase out animal testing for the purposes of chemical regulation. Meanwhile the number of commercially available chemicals and the requirements for hazard assessments have both increased, creating a large need for substitution of traditional in vivo assays with in vitro tests. One example of this is the replacement of the OECD acute toxicity test of adult fish (test guideline [TG] 203) with zebrafish embryos (TG 236). With new insights into the toxicological properties of chemicals, the demand on these replacement tests is also changing character with a shifted focus towards mechanistic understanding of toxicity. The omics sciences encompass a group of analytical methods which have proven to be very powerful for unveiling of mechanistic information of biochemical processes. Metabolomics is one of the younger members of this family and entails the large-scale analysis of endogenous metabolites and their perturbation in living organisms. The overall objective of this thesis was to develop modifications to the TG236 OECD assay to obtain omic data suitable for use in chemical hazard assessment. To achieve this goal, we started by developing a targeted and non-targeted metabolomics workflow and evaluated the performance of the two types of analysis (Paper I). We also evaluated the efficiency of three signal drift correction approaches, which is an important step in data quality improvement for non-targeted analysis, and reported previously unlisted biochemicals present in NIST reference material. In Paper II we applied the workflow in Paper I to a newly developed, in-plate extraction method for single zebrafish embryos which were exposed to the pharmaceutical and environmental pollutant propranolol. Data processing workflows were developed to overcome challenges arising from the occurrence of the exposure compound and its biotransformation products (or in-source fragments of these) in the

Over the last decade environmental agencies worldwide have escalated their work to phase out animal testing for the purposes of chemical regulation. Meanwhile the number of commercially available chemicals and the requirements for hazard assessments have both increased, creating a large need for substitution of traditional in vivo assays with in vitro tests. One example of this is the replacement of the OECD acute toxicity test of adult fish (test guideline [TG] 203) with zebrafish embryos (TG 236). With new insights into the toxicological properties of chemicals, the demand on these replacement tests is also changing character with a shifted focus towards mechanistic understanding of toxicity. The omics sciences encompass a group of analytical methods which have proven to be very powerful for unveiling of mechanistic information of biochemical processes. Metabolomics is one of the younger members of this family and entails the large-scale analysis of endogenous metabolites and their perturbation in living organisms. The overall objective of this thesis was to develop modifications to the TG236 OECD assay to obtain omic data suitable for use in chemical hazard assessment. To achieve this goal, we started by developing a targeted and non-targeted metabolomics workflow and evaluated the performance of the two types of analysis (Paper I). We also evaluated the efficiency of three signal drift correction approaches, which is an important step in data quality improvement for non-targeted analysis, and reported previously unlisted biochemicals present in NIST reference material. In Paper II we applied the workflow in Paper I to a newly developed, in-plate extraction method for single zebrafish embryos which were exposed to the pharmaceutical and environmental pollutant propranolol. Data processing workflows were developed to overcome challenges arising from the occurrence of the exposure compound and its biotransformation products (or in-source fragments of these) in the

A catalyst system comprising of pyrazolylpyridineamine/Cu(I)/CsOH is reported. for the hydroxylation of aryl iodides and bromides with moderate to outstanding yields, without the use of an inert atmosphere. A comprehensive parameter optimisation study established optimum component concentrations: [Cu(MeCN)4]BF4 and 2-(1H-pyrazol-1-yl)-N-(pyridine-2-ylmethyl)ethan-1-amine (L01) (2 mol %), substrate (1 mmol), CsOH (4 mmol) and DMSO:H2O (1:1, 3 mL). Monitoring substrate conversion as a function of time revealed an induction period of 90 min, which could be eliminated through the initial in situ formation of the proposed [(L01)Cu-OH] intermediate. Eliminating the induction period resulted in complete conversion within one hour, with turnover numbers exceeding that of the benchmark catalyst system operating at an optimal catalyst loading of 0.05 mol %

A catalyst system comprising of pyrazolylpyridineamine/Cu(I)/CsOH is reported. for the hydroxylation of aryl iodides and bromides with moderate to outstanding yields, without the use of an inert atmosphere. A comprehensive parameter optimisation study established optimum component concentrations: [Cu(MeCN)4]BF4 and 2-(1H-pyrazol-1-yl)-N-(pyridine-2-ylmethyl)ethan-1-amine (L01) (2 mol %), substrate (1 mmol), CsOH (4 mmol) and DMSO:H2O (1:1, 3 mL). Monitoring substrate conversion as a function of time revealed an induction period of 90 min, which could be eliminated through the initial in situ formation of the proposed [(L01)Cu-OH] intermediate. Eliminating the induction period resulted in complete conversion within one hour, with turnover numbers exceeding that of the benchmark catalyst system operating at an optimal catalyst loading of 0.05 mol %

The hydroxylation of nonreactive C−H bonds can be easily catalyzed by a variety of metalloenzymes, especially cytochrome P450s (P450s). The mechanism of P450 mediated hydroxylation has been intensively studied, both experimentally and theoretically. However, understanding the regio‐ and stereoselectivities of substrates hydroxylated by P450s remains a great challenge. Herein, we use a multi‐scale modeling approach to investigate the selectivity of testosterone (TES) and dihydrotestosterone (DHT) hydroxylation catalyzed by two important P450s, CYP3A4 and CYP19A1. For CYP3A4, two distinct binding modes for TES/DHT were predicted by dockings and molecular dynamics simulations, in which the experimentally identified sites of metabolism of TES/DHT can access to the catalytic center. The regio‐ and stereoselectivities of TES/DHT hydroxylation were further evaluated by quantum mechanical and ONIOM calculations. For CYP19A1, we found that sites 1β, 2β and 19 can access the catalytic center, with the intrinsic reactivity 2β>1β>19. However, our ONIOM calculations indicate that the hydroxylation is favored at site 19 for both TES and DHT, which is consistent with the experiments and reflects the importance of the catalytic environment in determining the selectivity. Our study unravels the mechanism underlying the selectivity of TES/DHT hydroxylation mediated by CYP3A4 and CYP19A1 and is helpful for understanding the selectivity of other substrates that are hydroxylated by P450s., QC 20200523, Biology

Over the last decade environmental agencies worldwide have escalated their work to phase out animal testing for the purposes of chemical regulation. Meanwhile the number of commercially available chemicals and the requirements for hazard assessments have both increased, creating a large need for substitution of traditional in vivo assays with in vitro tests. One example of this is the replacement of the OECD acute toxicity test of adult fish (test guideline [TG] 203) with zebrafish embryos (TG 236). With new insights into the toxicological properties of chemicals, the demand on these replacement tests is also changing character with a shifted focus towards mechanistic understanding of toxicity. The omics sciences encompass a group of analytical methods which have proven to be very powerful for unveiling of mechanistic information of biochemical processes. Metabolomics is one of the younger members of this family and entails the large-scale analysis of endogenous metabolites and their perturbation in living organisms. The overall objective of this thesis was to develop modifications to the TG236 OECD assay to obtain omic data suitable for use in chemical hazard assessment. To achieve this goal, we started by developing a targeted and non-targeted metabolomics workflow and evaluated the performance of the two types of analysis (Paper I). We also evaluated the efficiency of three signal drift correction approaches, which is an important step in data quality improvement for non-targeted analysis, and reported previously unlisted biochemicals present in NIST reference material. In Paper II we applied the workflow in Paper I to a newly developed, in-plate extraction method for single zebrafish embryos which were exposed to the pharmaceutical and environmental pollutant propranolol. Data processing workflows were developed to overcome challenges arising from the occurrence of the exposure compound and its biotransformation products (or in-source fragments of these) in the

The hydroxylation of nonreactive C−H bonds can be easily catalyzed by a variety of metalloenzymes, especially cytochrome P450s (P450s). The mechanism of P450 mediated hydroxylation has been intensively studied, both experimentally and theoretically. However, understanding the regio‐ and stereoselectivities of substrates hydroxylated by P450s remains a great challenge. Herein, we use a multi‐scale modeling approach to investigate the selectivity of testosterone (TES) and dihydrotestosterone (DHT) hydroxylation catalyzed by two important P450s, CYP3A4 and CYP19A1. For CYP3A4, two distinct binding modes for TES/DHT were predicted by dockings and molecular dynamics simulations, in which the experimentally identified sites of metabolism of TES/DHT can access to the catalytic center. The regio‐ and stereoselectivities of TES/DHT hydroxylation were further evaluated by quantum mechanical and ONIOM calculations. For CYP19A1, we found that sites 1β, 2β and 19 can access the catalytic center, with the intrinsic reactivity 2β>1β>19. However, our ONIOM calculations indicate that the hydroxylation is favored at site 19 for both TES and DHT, which is consistent with the experiments and reflects the importance of the catalytic environment in determining the selectivity. Our study unravels the mechanism underlying the selectivity of TES/DHT hydroxylation mediated by CYP3A4 and CYP19A1 and is helpful for understanding the selectivity of other substrates that are hydroxylated by P450s., QC 20200523, Biology

The hydroxylation of nonreactive C−H bonds can be easily catalyzed by a variety of metalloenzymes, especially cytochrome P450s (P450s). The mechanism of P450 mediated hydroxylation has been intensively studied, both experimentally and theoretically. However, understanding the regio‐ and stereoselectivities of substrates hydroxylated by P450s remains a great challenge. Herein, we use a multi‐scale modeling approach to investigate the selectivity of testosterone (TES) and dihydrotestosterone (DHT) hydroxylation catalyzed by two important P450s, CYP3A4 and CYP19A1. For CYP3A4, two distinct binding modes for TES/DHT were predicted by dockings and molecular dynamics simulations, in which the experimentally identified sites of metabolism of TES/DHT can access to the catalytic center. The regio‐ and stereoselectivities of TES/DHT hydroxylation were further evaluated by quantum mechanical and ONIOM calculations. For CYP19A1, we found that sites 1β, 2β and 19 can access the catalytic center, with the intrinsic reactivity 2β>1β>19. However, our ONIOM calculations indicate that the hydroxylation is favored at site 19 for both TES and DHT, which is consistent with the experiments and reflects the importance of the catalytic environment in determining the selectivity. Our study unravels the mechanism underlying the selectivity of TES/DHT hydroxylation mediated by CYP3A4 and CYP19A1 and is helpful for understanding the selectivity of other substrates that are hydroxylated by P450s., QC 20200523, Biology

The hydroxylation of nonreactive C−H bonds can be easily catalyzed by a variety of metalloenzymes, especially cytochrome P450s (P450s). The mechanism of P450 mediated hydroxylation has been intensively studied, both experimentally and theoretically. However, understanding the regio‐ and stereoselectivities of substrates hydroxylated by P450s remains a great challenge. Herein, we use a multi‐scale modeling approach to investigate the selectivity of testosterone (TES) and dihydrotestosterone (DHT) hydroxylation catalyzed by two important P450s, CYP3A4 and CYP19A1. For CYP3A4, two distinct binding modes for TES/DHT were predicted by dockings and molecular dynamics simulations, in which the experimentally identified sites of metabolism of TES/DHT can access to the catalytic center. The regio‐ and stereoselectivities of TES/DHT hydroxylation were further evaluated by quantum mechanical and ONIOM calculations. For CYP19A1, we found that sites 1β, 2β and 19 can access the catalytic center, with the intrinsic reactivity 2β>1β>19. However, our ONIOM calculations indicate that the hydroxylation is favored at site 19 for both TES and DHT, which is consistent with the experiments and reflects the importance of the catalytic environment in determining the selectivity. Our study unravels the mechanism underlying the selectivity of TES/DHT hydroxylation mediated by CYP3A4 and CYP19A1 and is helpful for understanding the selectivity of other substrates that are hydroxylated by P450s., QC 20200523, Biology

Over the last decade environmental agencies worldwide have escalated their work to phase out animal testing for the purposes of chemical regulation. Meanwhile the number of commercially available chemicals and the requirements for hazard assessments have both increased, creating a large need for substitution of traditional in vivo assays with in vitro tests. One example of this is the replacement of the OECD acute toxicity test of adult fish (test guideline [TG] 203) with zebrafish embryos (TG 236). With new insights into the toxicological properties of chemicals, the demand on these replacement tests is also changing character with a shifted focus towards mechanistic understanding of toxicity. The omics sciences encompass a group of analytical methods which have proven to be very powerful for unveiling of mechanistic information of biochemical processes. Metabolomics is one of the younger members of this family and entails the large-scale analysis of endogenous metabolites and their perturbation in living organisms. The overall objective of this thesis was to develop modifications to the TG236 OECD assay to obtain omic data suitable for use in chemical hazard assessment. To achieve this goal, we started by developing a targeted and non-targeted metabolomics workflow and evaluated the performance of the two types of analysis (Paper I). We also evaluated the efficiency of three signal drift correction approaches, which is an important step in data quality improvement for non-targeted analysis, and reported previously unlisted biochemicals present in NIST reference material. In Paper II we applied the workflow in Paper I to a newly developed, in-plate extraction method for single zebrafish embryos which were exposed to the pharmaceutical and environmental pollutant propranolol. Data processing workflows were developed to overcome challenges arising from the occurrence of the exposure compound and its biotransformation products (or in-source fragments of these) in the