Site Of Bond Cleavage Research Articles

Deeper Defluorination and Mineralization of a Novel PFECA (C7 HFPO-TA) in Vacuum UV/Sulfite: Unique Mechanism of H/OCF3 Exchange.

C7 HFPO-TA is a newly identified alternative to PFOA, which possesses a unique structure fragment (CF3O-CF(CF3)-). In this study, we evaluated the chemical reactivity of C7 HFPO-TA in advanced oxidation and reduction processes for the first time, which revealed a series of unexpected transformation mechanisms. The results showed that reductive degradation based on hydrated electrons (eaq-) was more feasible for the degradation of C7 HFPO-TA. For oxidative degradation, the branched -CF3 at the α-position carbon posed as the spatial hindrance, shielding the attack of SO4•- to -COO-. The synergistic effects of HO•/eaq- and direct photolysis led to deeper defluorination and mineralization of C7 HFPO-TA in the vacuum UV/sulfite (VUV/SF) process. We identified a unique H/OCF3 exchange that converted the CF3O-CF(CF3)- into H-CF(CF3)- directly, and the SO3•- involved mechanism of C7 HFPO-TA for the first time. We revealed the branched -CF3 connected to the same carbon next to the CF3O- group affected the C-O bond cleavage site, preferring the H/OCF3 exchange pathway. The defluorination of C7 HFPO-TA was compared with PFOA and three PFECAs in the VUV/SF process, which was highly dependent on structures. Degradation kinetics, theoretical calculations, and products' analysis provided an in-depth perspective on the degradation mechanisms and pathways of C7 HFPO-TA.

Mouse skin peptidomic analysis of the hemorrhage induced by a snake venom metalloprotease.

Hemorrhage induced by snake venom metalloproteases (SVMPs) results from proteolysis, capillary disruption, and blood extravasation. HF3, a potent SVMP of Bothrops jararaca, induces hemorrhage at pmol doses in the mouse skin. To gain insight into the hemorrhagic process, the main goal of this study was to analyze changes in the skin peptidome generated by injection of HF3, using approaches of mass spectrometry-based untargeted peptidomics. The results revealed that the sets of peptides found in the control and HF3-treated skin samples were distinct and derived from the cleavage of different proteins. Peptide bond cleavage site identification in the HF3-treated skin showed compatibility with trypsin-like serine proteases and cathepsins, suggesting the activation of host proteinases. Acetylated peptides, which originated from the cleavage at positions in the N-terminal region of proteins in both samples, were identified for the first time in the mouse skin peptidome. The number of peptides acetylated at the residue after the first Met residue, mostly Ser and Ala, was higher than that of peptides acetylated at the initial Met. Proteins cleaved in the hemorrhagic skin participate in cholesterol metabolism, PPAR signaling, and in the complement and coagulation cascades, indicating the impairment of these biological processes. The peptidomic analysis also indicated the emergence of peptides with potential biological activities, including pheromone, cell penetrating, quorum sensing, defense, and cell-cell communication in the mouse skin. Interestingly, peptides generated in the hemorrhagic skin promoted the inhibition of collagen-induced platelet aggregation and could act synergistically in the local tissue damage induced by HF3.

N-Formimidoylation/-iminoacetylation modification in aminoglycosides requires FAD-dependent and ligand-protein NOS bridge dual chemistry

Oxidized cysteine residues are highly reactive and can form functional covalent conjugates, of which the allosteric redox switch formed by the lysine-cysteine NOS bridge is an example. Here, we report a noncanonical FAD-dependent enzyme Orf1 that adds a glycine-derived N-formimidoyl group to glycinothricin to form the antibiotic BD-12. X-ray crystallography was used to investigate this complex enzymatic process, which showed Orf1 has two substrate-binding sites that sit 13.5 Å apart unlike canonical FAD-dependent oxidoreductases. One site could accommodate glycine and the other glycinothricin or glycylthricin. Moreover, an intermediate-enzyme adduct with a NOS-covalent linkage was observed in the later site, where it acts as a two-scissile-bond linkage facilitating nucleophilic addition and cofactor-free decarboxylation. The chain length of nucleophilic acceptors vies with bond cleavage sites at either N–O or O–S accounting for N-formimidoylation or N-iminoacetylation. The resultant product is no longer sensitive to aminoglycoside-modifying enzymes, a strategy that antibiotic-producing species employ to counter drug resistance in competing species.

Photodegradation study of the fenvalerate insecticide by 1H NMR, 13C NMR, and GC-MS and structural elucidation of its transformation products

The photolysis of fenvalerate, a pyrethroid insecticide, was studied in acetonitrile by 1H nuclear magnetic resonance (NMR) and 13C NMR to identify the site of bond cleavage and gas chromatography-mass spectrometry (GC-MS) to establish the chemical structure of fenvalerate photoproducts. Ultraviolet (UV) irradiation of fenvalerate solutions was performed for 18 h with a solar light simulator, and the photolysis reaction obeyed first-order kinetics. Photolysis half-life time (t1/2) values ranged between 15.25 and 21.63 h (mean photodegradation percentage = 51.7 %) for 1H NMR and between 4.55 and 8.06 h (mean photodegradation percentage > 80 %) for 13C NMR. We observed five sites of bond cleavage, namely carbonyl-tertiary carbon, tertiary carbon-tertiary carbon, carbonyl-oxygen, carboxyl-tertiary carbon, and aromatic carbon-tertiary carbon, yielding photoproducts formation. GC-MS was associated with 1H NMR and 13C NMR to obtain a complete photodegradation mechanism. Before UV irradiation, two chromatogram peaks were obtained, due to the two fenvalerate isomers. Under irradiation, both peaks decreased, and new peaks appeared, corresponding to photoproduct formation. After a 12- to 13-h irradiation, 99.39 % of fenvalerate was degraded with a mean rate constant of 0.305 h–1. The chemical structure of the formed photoproducts was identified, either by using the National Institute of Standards and Technology (NIST) mass spectral database or by interpreting the mass spectra. Finally, a detailed mechanism was proposed for fenvalerate photodegradation.

Domain-Dependent Evolution Explains Functional Homology of Protostome and Deuterostome Complement C3-Like Proteins.

Complement proteins emerged early in evolution but outside the vertebrate clade they are poorly characterized. An evolutionary model of C3 family members revealed that in contrast to vertebrates the evolutionary trajectory of C3-like genes in cnidarian, protostomes and invertebrate deuterostomes was highly divergent due to independent lineage and species-specific duplications. The deduced C3-like and vertebrate C3, C4 and C5 proteins had low sequence conservation, but extraordinarily high structural conservation and 2-chain and 3-chain protein isoforms repeatedly emerged. Functional characterization of three C3-like isoforms in a bivalve representative revealed that in common with vertebrates complement proteins they were cleaved into two subunits, b and a, and the latter regulated inflammation-related genes, chemotaxis and phagocytosis. Changes within the thioester bond cleavage sites and the a-subunit protein (ANATO domain) explained the functional differentiation of bivalve C3-like. The emergence of domain-related functions early during evolution explains the overlapping functions of bivalve C3-like and vertebrate C3, C4 and C5, despite low sequence conservation and indicates that evolutionary pressure acted to conserve protein domain organization rather than the primary sequence.

Multiple strategies of porous tetrametallene for efficient ethanol electrooxidation

The first synthesized porous Pd59W8Rh19Bi14 metallene combines OH adsorption effects, electronic effects and C–C bond cleavage site strategies to improve EOR performance. The metallene stable structure further accelerates the mass transfer rate.

Size Dependent Fragmentation Chemistry of Short Doubly Protonated Tryptic Peptides.

Tandem mass spectrometry of electrospray ionized multiply charged peptide ions is commonly used to identify the sequence of peptide(s) and infer the identity of source protein(s). Doubly protonated peptide ions are consistently the most efficiently sequenced ions following collision-induced dissociation of peptides generated by tryptic digestion. While the broad characteristics of longer (N ≥ 8 residue) doubly protonated peptides have been investigated, there is comparatively little data on shorter systems where charge repulsion should exhibit the greatest influence on the dissociation chemistry. To address this gap and further understand the chemistry underlying collisional-dissociation of doubly charged tryptic peptides, two series of analytes ([GxR+2H]2+ and [AxR+2H]2+, x = 2-5) were investigated experimentally and with theory. We find distinct differences in the preference of bond cleavage sites for these peptides as a function of size and to a lesser extent composition. Density functional calculations at two levels of theory predict that the threshold relative energies required for bond cleavages at the same site for peptides of different size are quite similar (for example, b2-yN-2). In isolation, this finding is inconsistent with experiment. However, the predicted extent of entropy change of these reactions is size dependent. Subsequent RRKM rate constant calculations provide a far clearer picture of the kinetics of the competing bond cleavage reactions enabling rationalization of experimental findings. The M06-2X data were substantially more consistent with experiment than were the B3LYP data.

Origin and Prediction of Highly Specific Bond Cleavage Sites in the Thermal Activation of Intact Protein Ions.

Predicting the fragmentation patterns of proteins would be beneficial for the reliable identification of intact proteins by mass spectrometry. However, the ability to accurately make such predictions remains elusive. An approach to predict the specific cleavage sites in whole proteins resulting from collision-induced dissociation by use of an improved electrostatic model for calculating the proton configurations of highly-charged protein ions is reported. Using ubiquitin, cytochrome c, lysozyme and β-lactoglobulin as prototypical proteins, this approach can be used to predict the fragmentation patterns of intact proteins. For sufficiently highly charged proteins, specific cleavages occur near the first low-basicity amino acid residues that are protonated with increasing charge state. Hybrid QM/QM' (QM=quantum mechanics) and molecular dynamics (MD) simulations and energy-resolved collision-induced dissociation measurements indicated that the barrier to the specific dissociation of the protonated amide backbone bond is significantly lower than competitive charge remote fragmentation. Unlike highly charged peptides, the protons at low-basicity sites in highly charged protein ions can be confined to a limited sequence of low-basicity amino acid residues by electrostatic repulsion, which results in highly specific fragmentation near the site of protonation. This research suggests that the optimal charge states to form specific sequence ions of intact proteins in higher abundances than the use of less specific ion dissociation methods can be predicted a priori.

AgII‐Mediated Synthesis of β‐Fluoroketones by Oxidative Cyclopropanol Opening

A regioselective synthesis of β‐fluorinated ketones by silver(II)‐mediated ring opening is described. Commercially available AgF2 serves as both an oxidant and fluorine‐atom source. A variety of β‐fluorinated ketones are efficiently prepared from tertiary cyclopropanol precursors, offering a straightforward approach for the introduction of a fluorine atom at a remote site. Selectivity is observed in the site of bond cleavage, which leads to fluorination at the more substituted site. A radical mediated sequential homolytic C–C bond cleavage and C–F bond formation is suggested.

Electron-induced dissociation (EID) for structure characterization of glycerophosphatidylcholine: determination of double-bond positions and localization of acyl chains.

Glycerophospholipids are a highly abundant and diverse collection of biologically relevant lipids, and distinction between isomeric and isobaric species is a fundamental aspect for confident identification. The ability to confidently assign a unique structure to a glycerophospholipid of interest is dependent on determining the number and location of the points of unsaturation and assignment of acyl chain position. The use of high-energy electrons (>20 eV) to induce gas-phase dissociation of intact precursor ions results in diagnostic product ions for localizing double-bond positions and determining acyl chain assignment. We describe a high-resolution, tandem mass spectrometry method for structure characterization of glycerophospholipids using electron-induced dissociation (EID). Furthermore, the inclusion of nomenclature to systematically assign bond cleavage sites with acyl chain position and double-bond location enables a uniform platform for lipid identification. The EID methodology detailed here combines novel application of an electron-based dissociation technique with high-resolution mass spectrometry that facilitates a new experimental approach for lipid biomarker discovery and validation.

Regiodivergent cyclobutanone cleavage: switching selectivity with different Lewis acids.

The exploitation of strain release in small rings as driving force to enable complex transformations is a powerful synthetic tool. Among them, cyclobutanones are particularly versatile substrates that can be elaborated in a wide variety of structurally diverse building blocks. Herein, Lewis acid catalyzed rearrangement reactions are presented that provide selective access to two structurally distinct polycyclic scaffolds, that is, indenylacetic acid derivatives and benzoxabicyclo[3.2.1]octan-3-ones. The choice of the Lewis acid fully controls the reaction pathway and the regioselectivity of the cyclobutanone CC bond cleavage site.

Can density functional theory (DFT) be used as an aid to a deeper understanding of tandem mass spectrometric fragmentation pathways?

Prediction of tandem mass spectrometric (MS/MS) fragmentation for non-peptidic molecules based on structure is of immense interest to the mass spectrometrist. If a reliable approach to MS/MS prediction could be achieved its impact within the pharmaceutical industry could be immense. Many publications have stressed that the fragmentation of a molecular ion or protonated molecule is a complex process that depends on many parameters, making prediction difficult. Commercial prediction software relies on a collection of general heuristic rules of fragmentation, which involve cleaving every bond in the structure to produce a list of 'expected' masses which can be compared with the experimental data. These approaches do not take into account the thermodynamic or molecular orbital effects that impact on the molecule at the point of protonation which could influence the potential sites of bond cleavage based on the structural motif. A series of compounds have been studied by examining the experimentally derived high-resolution MS/MS data and comparing it with the in silico modelling of the neutral and protonated structures. The effect that protonation at specific sites can have on the bond lengths has also been determined. We have calculated the thermodynamically most stable protonated species and have observed how that information can help predict the cleavage site for that ion. The data have shown that this use of in silico techniques could be a possible way to predict MS/MS spectra.

Active-site Mapping of a Populus Xyloglucan endo-Transglycosylase with a Library of Xylogluco-oligosaccharides

Restructuring the network of xyloglucan (XG) and cellulose during plant cell wall morphogenesis involves the action of xyloglucan endo-transglycosylases (XETs). They cleave the XG chains and transfer the enzyme-bound XG fragment to another XG molecule, thus allowing transient loosening of the cell wall and also incorporation of nascent XG during expansion. The substrate specificity of a XET from Populus (PttXET16-34) has been analyzed by mapping the enzyme binding site with a library of xylogluco-oligosaccharides as donor substrates using a labeled heptasaccharide as acceptor. The extended binding cleft of the enzyme is composed of four negative and three positive subsites (with the catalytic residues between subsites -1 and +1). Donor binding is dominated by the higher affinity of the XXXG moiety (G=Glcbeta(1-->4) and X=Xylalpha(1-->6)Glcbeta(1-->4)) of the substrate for positive subsites, whereas negative subsites have a more relaxed specificity, able to bind (and transfer to the acceptor) a cello-oligosaccharyl moiety of hybrid substrates such as GGGGXXXG. Subsite mapping with k(cat)/K(m) values for the donor substrates showed that a GG-unit on negative and -XXG on positive subsites are the minimal requirements for activity. Subsites -2 and -3 (for backbone Glc residues) and +2' (for Xyl substitution at Glc in subsite +2) have the largest contribution to transition state stabilization. GalGXXXGXXXG (Gal=Galbeta(1-->4)) is the best donor substrate with a "blocked" nonreducing end that prevents polymerization reactions and yields a single transglycosylation product. Its kinetics have unambiguously established that the enzyme operates by a ping-pong mechanism with competitive inhibition by the acceptor.

Tandem mass spectrometry and hydrogen/deuterium exchange studies of protonated species of 1,1′‐bis(diphenylphosphino)‐ferrocene oxidative impurity generated during a Heck reaction

Oxidation of 1,1'-bis(diphenylphosphino)-ferrocene (DPPF) was found to occur when it served as the ligand for Pd(II)(CH3COO)2 in a Heck reaction. This oxidative impurity of DPPF, referred to as DPPF(O), was identified by high-performance liquid chromatography/tandem mass spectrometry (HPLC/MS/MS) and exact mass measurements. Protonated DPPF(O) exhibited unique fragmentation pathways in the gas phase. Hydrogen/deuterium (H/D) exchange experiments provided important insights into the dissociation mechanisms of protonated DPPF(O), suggesting the existence of isomeric structures of the product ions by retaining or losing a proton (or deuteron) upon collision-induced dissociation (CID). The specific fate of the proton (or deuteron) upon CID is postulated to be dependent on the distance between the exchangeable proton (or deuteron) and the sites of bond cleavage. Density functional theory (DFT) calculations at the B3LYP/LANL2DZ level of theory showed that oxygen in DPPF(O) plays a pivotal role in invoking pi-cation interactions between the p-type lone pair electrons (n pi) in oxygen and the anti-bonding orbital of Fe(II), accounting for the major fragmentation pathways of protonated DPPF(O). Facile formation of organometallic distonic ions in dissociation of protonated DPPF(O), and especially of protonated DPPF, could be useful for further exploration of their chemical properties by gas-phase ion/molecule reactions.

Substituent effect on the reductive N-dearylation of 3-(indol-1-yl)-1,2-benzisoxazoles by rat liver microsomes.

The reductive metabolism of a series of 3-(indol-1-yl)-1,2-benzisoxazoles was examined in vitro using rat liver microsomes. 3-(Indol-1-yl)-1,2-benzisoxazole was reduced to the corresponding amidine (resulting from N-O bond cleavage) under anaerobic conditions. The reaction required viable microsomes and NADPH and was inhibited by carbon monoxide, air, and ketoconazole, suggesting the involvement of cytochrome p450 enzymes. The amidine was subsequently nonenzymatically hydrolyzed to 1-salicylindole, which in turn was hydrolyzed to indole. Addition of electron-withdrawing substituents (Cl-, MeSO2-) at the 6-position of the benzisoxazole ring resulted in a significant increase in the rate of substrate reduction. Introduction of electron-withdrawing substituents on the indole ring likewise increased the rate of substrate consumption but caused a substituent-dependent shift of the site of bond cleavage from the 1,2-isoxazole N-O bond to the C-N bond linking the 1,2-benzisoxazole to the indole moiety. In the case of 3-(2-chloro-3-methanesulfoxylindol-1-yl)-1,2-benzisoxazole, C-N bond cleavage was nearly quantitative, and products resulting from N-O bond reduction were not observed. The overall rates of 3-(indol-1-yl)-1,2-benzisoxazoles reduction were found to be substrate concentration-dependent and observed Michaelis-Menten-type behavior. The apparent Vmax of substrate reduction by rat liver microsomes correlated negatively with the free energy of the lowest unoccupied molecular orbitals (ELUMO) calculated semiempirically using a parameterized model 3 (PM3), and suggested that the initial electron transfer was rate-determining and that the ELUMO could be used as an indication of the susceptibility of 1,2-isoxazoles to undergo reductive metabolism.

Phosphotriesterase: an enzyme in search of its natural substrate.

The bacterial PTE is able to catalyze the hydrolysis of a wide range of organophosphate nerve agents. The active site has been shown to consist of a unique binuclear metal center that has evolved to deliver hydroxide to the site of bond cleavage. The reaction rate for the hydrolysis of activated substrates such as paraoxon is limited by product release or an associated protein conformational change.

Synthesis of 1,3-dioxolanes by the addition of ketones to epoxides by using [Cp*Ir(NCMe)3]2+ as catalyst

Abstract A series of 1,3-dioxolanes have been prepared by the addition of ketones to epoxides in the presence of the catalyst [Cp*Ir(NCMe)3]2+, Cp*C5Me5. The reactions proceed readily at 22°C and the yields are good. The following 1,3-dioxolanes: 2,2,4-trimethyl-1,3-dioxolane, 1; 2,2-dimethyl-4-vinyl-1,3-dioxolane, 2; 2,2-dimethyl-4-phenyl-1,3-dioxolane, 3; 2,2-diethyl-4-methyl-1,3-dioxolane, 4; 2,2-diethyl-4-vinyl-1,3-dioxolane, 5; 2,2-diethyl-4-phenyl-1,3-dioxolane, 6 were prepared from the appropriate epoxide and carbonyl compounds. An inversion of configuration at the carbon atom at the C–O bond cleavage site of the epoxide was observed to occur in the formation of the dioxolanes: R, S,- 2,2,4,5-tetramethyl-1,3-dioxolane, 7 and a mixture of R,R- and S,S-2,2,4,5-tetramethyl-1,3-dioxolane, 8 obtained from the reactions of acetone with R, R,-/S, S,-buten-2-oxide and R, S,-buten-2-oxide, respectively.

Kinetics of the Hydrodenitrogenation of Decahydroquinoline over NiMo(P)/Al2O3Catalysts

Cis- and trans-propylcyclohexylamine were identified as primary reaction intermediates of the aliphatic C−N bond cleavage in the hydrodenitrogenation (HDN) network of decahydroquinoline (DHQ). The kinetic parameters of the HDN network were calculated assuming a Langmuir−Hinshelwood mechanism. Three kinds of catalytic sites could be distinguished: aliphatic C(sp3)−N bond cleavage, (de)hydrogenation of a (aromatic) heterocyclic ring, and alkene hydrogenation. The adsorption constants over NiMo/Al2O3 and NiMoP/Al2O3 catalysts were the same for the C(sp3)−N bond cleavage site, while different for the hydrogenation sites. The decreased rate constant of the first C(sp3)−N bond cleavage accounts for the negative effect of phosphorus in the HDN of DHQ. Introduction of Ni to a Mo(P)/Al2O3 catalyst increased the rate constant of the C(sp3)−N bond cleavage by a factor of 2, and that of alkene hydrogenation by a factor of 6.

Determination of Sequence Specificity between a Plasmid Replication Initiator Protein and the Origin of Replication

Staphylococcal plasmids of the pT181 family replicate by a rolling circle mechanism, requiring the activities of a plasmid-specified Rep protein. The initiation event involves site-specific phosphodiester bond cleavage by Rep within the replication origin, ori. In vitrothe Rep proteins also display type-I topoisomerase activity specific for this plasmid family. Although the single site of bond cleavage, ICR II, is conserved among all members of the pT181 family, the plasmid-specific Rep proteins are able to discriminate between family members in vivo, initiating replication only from the cognate origin. The basis of such specificity is believed to be due to a non-covalent binding interaction between Rep and a DNA sequence adjacent to the site of phosphodiester bond cleavage. Using the RepD protein specified by plasmid pC221, we present data for the physical parameters of RepD: oriDcomplex formation. Quantification of the relative strengths of the non-covalent interactions for different but related oritarget sequences, measured by gel mobility shift experiments, has yielded data that are in accord with the known specificity of the protein in vivo. Oligonucleotide competition experiments demonstrate that this interaction is indeed attributable to the specificity determinant, ICR III. Protein-DNA crosslinking methods show that a carboxyl-terminal proteolytic fragment of RepD makes a specific interaction with the ICR III region of its cognate replication origin. Analysis of topoisomerase rates indicates that the interaction between ICR III and the carboxyl terminus of the protein is required before a productive interaction, namely the phosphodiester bond cleavage at the ICR II, can occur.

Base hydrolysis in homometallic dinuclear chromium(III) complexes bridged by hydroxide and carboxylate

Base hydrolysis of dinuclear complexes [Cr2(µ-OH)(µ-RCO2)(en)4]4+ and [(nta)Cr(µ-OH)(µ-RCO2)Cr(en)2]+(en = ethane-1,2-diamine, nta = nitrilotriacetate; R = H, Me, Et, Prn, CH2Cl, CH2ClCH2, MeOCH2 or Ph) was studied by using the UV/VIS absorption and 2H NMR spectral changes and chromatography. The reactions were found to occur in two stages: the first-stage rates (k1) varied with R, but the second-stage ones (k2) were almost the same throughout the series. Analysis of the kinetic data for the two types of complexes disclosed the effects of the substituent groups R and/or the non-bridging ligands on the carboxylato bridge-cleavage reaction mechanism. Examination of the substituent effects in terms of Taft's equation with the electronic (ρ*) and steric (δ) parameters gave a critical clue to establishing the difference in bond-cleavage sites. The values were ρ*= 2.29 ± 0.20 and δ= 1.41 ± 0.13 for [Cr2(µ-OH)(µ-RCO2)(en)4]4+ and ρ*= 0.01 ± 0.11 and δ= 0.32 ± 0.08 for [(nta)Cr(µ-OH)(µ-RCO2)Cr(en)2]+. The carboxylato bridge-cleavage reaction is influenced by both the inductive and steric effects of the substituents in [Cr2(µ-OH)(µ-RCO2)(en)4]4+, and both effects contribute to smaller extents for [(nta)Cr(µ-OH)(µ-RCO2)Cr(en)2]+; the former complexes undergo cleavage at the carboxylic acyl C–O bond and the latter at the Cr–O bond in the Cr(en)2 site.