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Mechanistic Pathways (mechanistic + pathway)
Kinds of Mechanistic Pathways Selected AbstractsIntramolecular Endo-Dig Hydrosilylation Catalyzed by Ruthenium: Evidence for a New Mechanistic Pathway.CHEMINFORM, Issue 22 2003Barry M. Trost Abstract For Abstract see ChemInform Abstract in Full Text. [source] Copper(II)-Mediated Aromatic ortho -Hydroxylation: A Hybrid DFT and Ab Initio ExplorationCHEMISTRY - A EUROPEAN JOURNAL, Issue 1 2008Peter Comba Prof. Dr. Abstract Mechanistic pathways for the aromatic hydroxylation by [CuII(L1)(TMAO)(O)], (L1=hippuric acid, TMAO=trimethylamine N -oxide), derived from the ON bond homolysis of its [CuII(L1)(TMAO)2] precursor, were explored by using hybrid density functional theory (B3LYP) and highly correlated ab initio methods (QCISD and CCSD). Published experimental studies suggest that the catalytic reaction is triggered by a terminal copper,oxo species, and a detailed study of electronic structures, bonding, and energetics of the corresponding electromers is presented. Two pathways, a stepwise and a concerted reaction, were considered for the hydroxylation process. The results reveal a clear preference for the concerted pathway, in which the terminal oxygen atom directly attacks the carbon atom of the benzene ring, leading to the ortho -selectively hydroxylated product. Solvent effects were probed by using the PCM and CPCM solvation models, and the PCM model was found to perform better in the present case. Excellent agreement between the experimental and computational results was found, in particular also for changes in reactivity with derivatives of L1. [source] On the Mechanism of Biotransformation of the Anthraquinonic Dye Acid Blue 62 by LaccasesADVANCED SYNTHESIS & CATALYSIS (PREVIOUSLY: JOURNAL FUER PRAKTISCHE CHEMIE), Issue 11-12 2009Luciana Pereira Abstract We used the recombinant CotA-laccase from the bacterium Bacillus subtilis to investigate the biotransformation of the commercial anthraquinonic dye Acid Blue 62. Kinetics of dye biotransformation at pH,6 follow a Michaelis,Menten model. NMR and several MS techniques allowed the identification of intermediates and final products of the enzymatic biotransformation. The main final product obtained, 1-[(4-amino-9,10-dioxo-3-sulfo-9,10-dihydroanthracen-1-yl)diazenyl]-4-cyclohexylamino-9,10-dioxo-9,10-dihydroanthracene-2-sulfonic acid, is formed through the creation of an azo link and has been previously identified as an intermediate compound in the biodegradation of Acid Blue 62 by crude fungal preparations. The identification of 1,4-diamino-9,10-dioxo-3-sulfo-9,10-dihydroanthracene-2-sulfonic acid and of cyclohexanone, in reaction mixtures with CotA-laccase and also its presence in reactions performed with the LAC3 laccase from the fungus Trametes sp. C30, suggest the occurrence of coupling reactions between the intermediate products of dye oxidation. Based on these results, we propose a mechanistic pathway for the biotransformation of Acid Blue 62 by laccases. A bioassay based on the inhibitory effects of the dye and its enzymatic products on the growth of Saccharomyces cerevisiae shows the importance of laccases in reducing dye toxicity. [source] Selectivity of nitro versus fluoro substitution in arenes in their reactions with charged O - and S -nucleophilesJOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 6 2007Irina A. Khalfina Abstract The relative mobility of nitro and fluoro substituents in 1,3-dinitro- and 1-fluoro-3-nitrobenzenes, 3,5-dinitro- and 3-fluoro-5-nitrobenzotrifluorides under the action of the nucleophiles (2ArYH)·K2CO3 and ArY,K+ in solution and the nucleophiles ArYH·K2CO3 (Y,=,O, S) under heterogeneous conditions was studied by a competitive method in DMF at 40,140,°C. The unique dependences of ,,H, on ,,S, and ,,H, on ,,G, were determined for all the substrates and nucleophiles. The dependence of the mechanistic pathway on the nucleophile is discussed. Two results are relevant to the reactions studied: (i) substituent effects in the nucleophiles (2ArYH)·K2CO3 and ArYH·K2CO3 on the activation entropies suggest that the entropy favours the displacement of nitro group; (ii) the negative signs of ,,H, and ,,S, for the reactions of the nucleophiles ArY,K+ indicate that the enthalpy determines the displacement of nitro group. It is concluded that the selectivity of the reactions with aryloxide and arylthioxide ions cannot be explained by the hard,soft acid,base principle only. Copyright © 2007 John Wiley & Sons, Ltd. [source] Structure of Escherichia coli pyridoxine 5,-phosphate oxidase in a tetragonal crystal form: insights into the mechanistic pathway of the enzymeACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2005Faik N. Musayev Escherichia coli pyridoxine 5,-phosphate oxidase (ePNPOx) catalyzes the terminal step in the biosynthesis of pyridoxal 5,-phosphate (PLP) by the FMN oxidation of pyridoxine 5,-phosphate (PNP) or pyridoxamine 5,-phosphate (PMP), forming FMNH2 and H2O2. The crystal structure of ePNPOx is reported in a tetragonal unit cell at 2.6,Å resolution. The three-dimensional fold of this structure is very similar to those of the E. coli and human enzymes that crystallized in trigonal and monoclinic unit cells. However, unlike the previous structures, the tetragonal structure shows major disorder in one of the two subunit domains that has opened up both the active site and a putative tunnel. Comparison of these structures gives an insight into the mechanistic pathway of PNPOx: from the resting enzyme with no substrate bound, to the initial binding of the substrate at the active site, to the catalytic stage and to the release of the catalytic product from the active site. [source] 2125: High glucose sensitizes human retinal endothelial cells for IFN-g-mediated apoptosisACTA OPHTHALMOLOGICA, Issue 2010R NAGARAJ Purpose The biochemical mechanisms by which inflammatory cytokines cause damage in the diabetic retina are poorly understood. Indoelamine 2, 3-dioxygenase (IDO) is an inducible by IFN-, enzyme and is the first enzyme of the kynurenine pathway, which produces cytotoxic kynurenines. In this study we have investigated the role of IDO in apoptosis of human retinal capillary endothelial cells (HREC) under hyperglycemic conditions. Methods HREC were cultured in medium containing high glucose (25 mM) or low glucose (7.5 mM) and incubated with 1-100 U/ml of IFN-,. IDO activity was measured by an HPLC assay. Expression of IFN-, receptor 1, and activation of the JAK-STAT signaling pathway along with activation of PKC-, was assessed by Western blotting. HREC apoptosis was measured by Hoechst staining. The role of IDO in HREC apoptosis was evaluated in the presence specific chemical inhibitors of the kynurenine pathway. Results IFN-, dose-dependently activated JAK-STAT signaling and PKC-,, and upregulated IDO. The IDO-mediated tryptophan oxidation led to formation of kynurenines, which was followed by chemical modification of proteins by kynurenines in HREC. These changes were accompanied by production of reactive oxygen species (ROS) and depletion of protein-free thiols. IFN-, inhibited cell cycle at low concentrations and caused caspase-3-mediated apoptosis and at higher concentrations, and those effects were amplified in the presence of high glucose in HREC. We found that IFN-, mediated cytotoxicity in HREC was primarily due to ROS generated by 3-hydroxykynurenine. Conclusion Our results suggest that high glucose sensitizes HREC to deleterious effects IFN-, and provide a novel mechanistic pathway for retinal capillary endothelial cell death in diabetes. [source] Multiple Reaction Pathways in Rhodium-Catalyzed Hydrosilylations of KetonesCHEMISTRY - A EUROPEAN JOURNAL, Issue 43 2009Nathanaëlle Schneider Dr. Abstract A detailed density functional theory (DFT) computational study (using the BP86/SV(P) and B3LYP/TZVP//BP86/SV(P) level of theory) of the rhodium-catalyzed hydrosilylation of ketones has shown three mechanistic pathways to be viable. They all involve the generation of a cationic complex [LnRhI]+ stabilized by the coordination of two ketone molecules and the subsequent oxidative addition of the silane, which results in the Rh,silyl intermediates [LnRhIII(H)SiHMe2]+. However, they differ in the following reaction steps: in two of them, insertion of the ketone into the RhSi bond occurs, as previously proposed by Ojima et,al., or into the SiH bond, as proposed by Chan et,al. for dihydrosilanes. The latter in particular is characterized by a very high activation barrier associated with the insertion of the ketone into the SiH bond, thereby making a new, third mechanistic pathway that involves the formation of a silylene intermediate more likely. This "silylene mechanism" was found to have the lowest activation barrier for the rate-determining step, the migration of a rhodium-bonded hydride to the ketone that is coordinated to the silylene ligand. This explains the previously reported rate enhancement for R2SiH2 compared to R3SiH as well as the inverse kinetic isotope effect (KIE) observed experimentally for the overall catalytic cycle because deuterium prefers to be located in the stronger bond, that is, CD versus MD. [source] Base-Induced Sequential Cyclization,Rearrangement of Enantioenriched 3-Aminoalkanoates to Five- and Seven-Membered LactamsCHEMISTRY - AN ASIAN JOURNAL, Issue 8-9 2008Takeo Sakai Abstract By treatment with tBuLi, linear 3-aminoalkanoates (4) were converted stereoselectively into five- and seven-membered lactams (trans- 5 and cis- 6). Initial cyclization to azetidin-2-one with subsequent aza-[1,2] and [2,3] rearrangement is the probable mechanistic pathway from 4 to 5 and 6. Although enantioenriched 4 was converted into nearly racemic 5 and 6, a linear 3-amino-2-methylalkanoate (17) with 90,%,ee bearing chirality at the ester ,-position afforded an all- cis seven-membered lactam (18) bearing three asymmetric centers with 85,%,ee. [source] Interstrand crosslink inducing agents in pretransplant conditioning therapy for hematologic malignanciesENVIRONMENTAL AND MOLECULAR MUTAGENESIS, Issue 6 2010Benigno C. Valdez Abstract Despite successful molecularly targeted, highly specific, therapies for hematologic malignancies, the DNA interstrand crosslinking agents, which are among the oldest and least specific cytotoxic drugs, still have an important role. This is particularly true in stem cell transplantation, where virtually every patient receives conditioning therapy with a DNA-alkylating agent-based program. However, due to concern about serious additive toxicities with combinations of different alkylating drugs, the last several years have seen nucleoside analogs, whose cytotoxic action follows vastly different molecular pathways, introduced in combination with alkylating agents. The mechanistic differences paired with different metabolic pathways for the respective drugs have clinically translated into increased safety without appreciable loss of antileukemic activity. In this report, we review pre-clinical evidence for synergistic antileukemic activity when nucleoside analog(s) and DNA-alkylating agent(s) are combined in the most appropriate manner(s), without a measurable decrease in clinical efficacy compared with the more established alkylating agent combinations. Data from our own laboratory using combinations of fludarabine, clofarabine, and busulfan as prototype representatives for these respective classes of cytotoxic agents are combined with information from other investigators to explain how the observed molecular events will result in greatly enhanced synergistic cytotoxicity. We further present possible mechanistic pathways for such desirable cytotoxic synergism. Finally, we propose how this information-backed hypothesis can be incorporated in the design of the next generation conditioning therapy programs in stem cell transplantation to optimize antileukemic efficacy while still safeguarding patient safety. Environ. Mol. Mutagen., 2010. © 2010 Wiley-Liss, Inc. [source] An Efficient Synthesis of Substituted meta -Halophenols and Their Methyl Ethers: Insight into the Reaction MechanismEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 15 2010Faiz Ahmed Khan Abstract An expeditious synthetic methodology leading to substituted meta -halophenols and their corresponding methyl ether derivatives through acid-mediated fragmentation of suitably substituted dihalonorbornyl ketones has been devised. The reaction sequence consists of TBTH-mediated (TBTH is tri- n -butyltin hydride) selective bridgehead halogen reduction of easily accessible Diels,Alder adducts derived from 1,2,3,4-tetrahalo-5,5-dimethoxycyclopentadiene and ,-substituted vinyl acetates, with subsequent conversion into the requisite bicyclic ketones by a two-step hydrolysis/oxidation approach. An extensive mechanistic investigation based on isotope labeling and cross experiments has been carried out and plausible mechanistic pathways based on these results have been proposed. The absence of halogen atoms at the bridgehead positions steers the reaction through a novel pathway involving the incorporation of proton (or deuterium) followed by elimination of HX (or DX), so the described methodology also provides a reliable route to ortho-para dideuteratedphenolic derivatives. [source] A Combined Theoretical and Experimental Research Project into the Aminolysis of ,-Lactam Antibiotics: The Importance of Bifunctional CatalysisEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 21 2003Natalia Díaz Abstract This paper reports the results of experimental work on the aminolysis of penicillin (6-APA) and monobactam (aztreonam) antibiotics by propylamine or ethanolamine. In general, aztreonam is slightly more reactive than 6-APA, despite the common assumption that the amide bond should be less activated in monobactams. Intriguingly, when ethanolamine acts as the nucleophile, the corresponding rate law has a kinetic term proportional to [RNH2][RNH3+]. To complement the experimental observations, the rate-determining free energy barriers in aqueous solution for various mechanistic pathways were computed by standard quantum chemical methodologies. From previous theoretical work it was assumed that the aminolysis of ,-lactams proceeds through mechanisms in which either a water molecule or a second amine molecule may act as bifunctional catalysts, assisting proton transfer from the attacking amine molecule to the leaving amino group. The energy barriers as computed have moderate values (ca. 26,34 kcal·mol,1) and reproduce most of the experimentally observed kinetic trends. Furthermore, the calculations predict that positively charged ethanolamine molecules can act as bifunctional catalysts as well, thus explaining the presence of the kinetic term proportional to [RNH2][RNH3+] in the rate law. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2003) [source] Pyrazole formation: Examination of kinetics, substituent effects, and mechanistic pathways,INTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 7 2008Joseph C. Sloop Reaction kinetics for the condensation of 1,3-diketones 1a,o with selected arylhydrazines (aryl = Ph, 4-NO2Ph, 4-CH3OPh, and 2,4-diNO2Ph) was studied using 19F NMR spectroscopy. Product regioselectivity is modulated by reactant ratios, substituents, and acidity. Reaction rates were found to be influenced by substituents on the diketones and on phenylhydrazines as well as by acidity of the reaction medium with rates varying as much as 1000-fold. Hammett , values for these cyclizations were determined. The reaction was found to be first order in both the diketone and arylhydrazine. The rate-determining step for pyrazole formation shifts as a function of pH. Mechanistic details and reaction pathways supporting these findings are proposed. © 2008 Wiley Periodicals, Inc. Int J Chem Kinet 40: 370,383, 2008 [source] N-Heterocyclic Carbene-Mediated Enantioselective Addition of Phenols to Unsymmetrical AlkylarylketenesADVANCED SYNTHESIS & CATALYSIS (PREVIOUSLY: JOURNAL FUER PRAKTISCHE CHEMIE), Issue 17 2009Carmen Concellón Abstract Chiral N-heterocyclic carbenes (NHCs) mediate the enantioselective addition of 2-phenylphenol to unsymmetrical alkylarylketenes, delivering ,-alkyl-,-arylacetic acid derivatives with good levels of enantiocontrol (up to 84% ee). Enantiodivergent stereochemical outcomes are observed using 2-phenylphenol and benzhydrol in the NHC-promoted esterification reaction using a triazolium precatalyst derived from pyroglutamic acid, consistent with distinct mechanistic pathways operating within these processes. [source] The mechanism of alkaline hydrolysis of amides: a comparative computational and experimental study of the hydrolysis of N -methylacetamide, N -methylbenzamide, and acetanilideJOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 6 2009Diana Cheshmedzhieva Abstract Theoretical computations and experimental kinetic measurements were applied in studying the mechanistic pathways for the alkaline hydrolysis of three secondary amides: N -methylbenzamide, N -methylacetamide, and acetanilide. Electronic structure methods at the HF/6-31+G(d,p) and B3LYP/6-31+G(d,p) levels of theory are employed. The energies of the stationary points along the reaction coordinate were further refined via single point computations at the MP2/6-31+G(d,p) and MP2/6-311++G(2d,2p) levels of theory. The role of water in the reaction mechanisms is examined. The theoretical results show that in the cases of N -methylbenzamide and N -methylacetamide the process is catalyzed by an ancillary water molecule. The influence of water is further assessed by predicting its role as bulk solvent. The alkaline hydrolysis process in aqueous solution is characterized by two distinct free energy barriers: the formation of a tetrahedral adduct and its breaking to products. The results show that the rate-determining stage of the process is associated with the second transition state. The entropy terms evaluated from theoretical computations referring to gas-phase processes are significantly overestimated. The activation barriers for the alkaline hydrolysis of N -methylbenzamide and acetanilide were experimentally determined. Quite satisfactory agreement between experimental values and computed activation enthalpies was obtained. Copyright © 2008 John Wiley & Sons, Ltd. [source] EPR study of nitroxides formed from the reaction of nitric oxide with photolyzed amidesMAGNETIC RESONANCE IN CHEMISTRY, Issue 9 2003Fan Wang Abstract Free radicals generated from UV irradiation of simple aliphatic amides in anaerobic and nitric oxide (NO)-saturated liquid mixtures or solutions gave EPR spectra of nitroxides. The application of isotopic effects to EPR spectra and the generation of radicals by transient radical attack on substrate molecules or by photolysing amine or acetoin were used to help identify photochemically produced radicals from the amides. The aliphatic amides used were formamide, acetamide and their N -methyl- or deuterium-substituted derivatives. Transient radicals used to attack the amides via hydrogen-atom abstraction were generated from the initiator AIBN or AAPH. The observation of various nitroxides indicates the reactivity of NO for trapping acyl, carbamoyl and other carbon-centered radicals. Possibly mechanistic pathways diagnosed with this trap are proposed. Copyright © 2003 John Wiley & Sons, Ltd. [source] Palladium(II)-catalyzed catalytic aminocarbonylation and alkoxycarbonylation of terminal alkynes: regioselectivity controlled by the nucleophilesAPPLIED ORGANOMETALLIC CHEMISTRY, Issue 1 2010Rami Suleiman Abstract The aminocarbonylation and alkoxycarbonylation reactions of terminal alkynes took place smoothly and efficiently using a catalyst system Pd(OAc)2,dppb,p -TsOHCH3CNCO under relatively mild experimental conditions. The catalytic system was tested and optimized using two different nucleophiles: alcohols and amines. Phenylacetylene (1a) was considered as an alkyne along with diisobutylamine (2b1) and methanol (2c1) as nucleophiles. The results showed significant differences in the conversion of 1a and in the selectivity towards the gem or trans unsaturated esters or amides with these nucleophiles. The effects of the type of palladium catalysts, the type of ligands, the amount of dppb and the solvents were carefully studied. With diisobutylamine (2b1), excellent regioselectivity towards the 2-acrylamides (gem isomer, 3ab1) was almost always observed, while trans -,,,-unsaturated esters 4ac1 was the predominant product with methanol (2c1) as a nucleophile. This remarkable sensitivity in the selectivity of the reaction indicates two different possible mechanistic pathways for these carbonylation reactions. Copyright © 2009 John Wiley & Sons, Ltd. [source] An Unexpected Michael,Aldol,Smiles Rearrangement Sequence for the Synthesis of Versatile Optically Active Bicyclic Structures by Using Asymmetric OrganocatalysisCHEMISTRY - A EUROPEAN JOURNAL, Issue 14 2010Nicole Holub Dr. Abstract A facile and simple organocatalytic procedure to generate optically active 6-alkyl- and 6-aryl-substituted bicyclo[2.2.2]oct-5-en-2-ones is presented. The reaction is catalysed by a 9-amino-9-deoxyepiquinine trifluoroacetic acid salt, which activates ,,,-unsaturated cyclic ketones for the 1,4-addition of ,-keto benzothiazoyl sulfones in a stereoselective fashion. Subsequent intramolecular aldol reaction and Smiles rearrangement gives rise to important optically active bicycles, which are a common motif in natural products, ligands in asymmetric catalysis and substrates for Cope rearrangements, photochemical reactions, radical cyclisations and metathesis. Different bicyclic structures were obtained by utilisation of various cyclic enones or by performing ring-expanding reactions. Furthermore, two possible mechanistic pathways are outlined and discussed. [source] Multiple Reaction Pathways in Rhodium-Catalyzed Hydrosilylations of KetonesCHEMISTRY - A EUROPEAN JOURNAL, Issue 43 2009Nathanaëlle Schneider Dr. Abstract A detailed density functional theory (DFT) computational study (using the BP86/SV(P) and B3LYP/TZVP//BP86/SV(P) level of theory) of the rhodium-catalyzed hydrosilylation of ketones has shown three mechanistic pathways to be viable. They all involve the generation of a cationic complex [LnRhI]+ stabilized by the coordination of two ketone molecules and the subsequent oxidative addition of the silane, which results in the Rh,silyl intermediates [LnRhIII(H)SiHMe2]+. However, they differ in the following reaction steps: in two of them, insertion of the ketone into the RhSi bond occurs, as previously proposed by Ojima et,al., or into the SiH bond, as proposed by Chan et,al. for dihydrosilanes. The latter in particular is characterized by a very high activation barrier associated with the insertion of the ketone into the SiH bond, thereby making a new, third mechanistic pathway that involves the formation of a silylene intermediate more likely. This "silylene mechanism" was found to have the lowest activation barrier for the rate-determining step, the migration of a rhodium-bonded hydride to the ketone that is coordinated to the silylene ligand. This explains the previously reported rate enhancement for R2SiH2 compared to R3SiH as well as the inverse kinetic isotope effect (KIE) observed experimentally for the overall catalytic cycle because deuterium prefers to be located in the stronger bond, that is, CD versus MD. [source] Structure Formation Principles and Reactivity of Organolithium CompoundsCHEMISTRY - A EUROPEAN JOURNAL, Issue 14 2009Viktoria Abstract Organolithium chemistry! An overview of the structure formation principles and the strong structure,reactivity relationship of lithium organics is given. By means of the commonly used lithium bases the deaggregation of the oligomeric parent structures to small adducts is presented (see examples) and compared to the related chemistry of lithiosilanes. The structure,reactivity relationship is an important feature of organolithium compounds. The knowledge of the structure of reactive species is crucial for the elucidation of reaction mechanisms and the understanding of observed selectivities. This concept article gives an overview over the structural principles of lithium organics and their Lewis base coordinated complexes in the solid state. The transition from the oligomeric parent structures to smaller adducts, such as dimers and monomers, as well as special degrees of aggregation is presented. Besides the commonly used alkyllithium compounds, a short overview over the structural principles of the higher homologous silyllithium compounds is given. Moreover, the structure,reactivity relationship is depicted by means of the reactivity of the Lewis bases towards intramolecular decomposition reactions with the organolithium compound. Selected examples confirm the importance of structure elucidation for the understanding of mechanistic pathways and selectivities. [source] Nickel-Catalyzed Mizoroki,Heck- versus Michael-Type Addition of Organoboronic Acids to ,,,-Unsaturated Alkenes through Fine-Tuning of LigandsCHEMISTRY - AN ASIAN JOURNAL, Issue 11 2007Pao-Shun Lin Abstract Various arylboronic acids reacted with activated alkenes in the presence of [Ni(dppe)Br2], ZnCl2, and H2O in CH3CN at 80,°C to give the corresponding Mizoroki,Heck-type addition products in good to excellent yields. Furthermore, 1,equivalent of the hydrogenation product of the activated alkene was also produced. By tuning the ligands of the nickel complexes and the reaction conditions, Michael-type addition was achieved in a very selective manner. Thus, various p- and o- substituted arylboronic acids or alkenylboronic acid reacted smoothly with activated alkenes in CH3CN at 80,°C for 12,h catalyzed by Ni(acac)2, P(o -anisyl)3, and K2CO3 to give the corresponding Michael-type addition products in excellent yields. However, for m- substituted arylboronic acids, the yields of Michael-type addition products are very low. The cause of this unusual meta -substitution effect is not clear. By altering the solvent or phosphine ligand, the product yields for m- substituted arylboronic acids were greatly improved. In contrast to previous results in the literature, the present catalytic reactions required water for Mizoroki,Heck-type products and dry reaction conditions for Michael-type addition products. Possible mechanistic pathways for both addition reactions are proposed. [source] |