Acid Rearrangement Research Articles

Factors influencing the rearrangement of bis-allylic hydroperoxides by manganese lipoxygenase

Manganese lipoxygenase (Mn-LOX) catalyzes the rearrangement of bis-allylic S-hydroperoxides to allylic R-hydroperoxides, but little is known about the reaction mechanism. 1-Linoleoyl-lysoglycerophosphatidylcholine was oxidized in analogy with 18:2n-6 at the bis-allylic carbon with rearrangement to C-13 at the end of lipoxygenation, suggesting a "tail-first" model. The rearrangement of bis-allylic hydroperoxides was influenced by double bond configuration and the chain length of fatty acids. The Gly316Ala mutant changed the position of lipoxygenation toward the carboxyl group of 20:2n-6 and 20:3n-3 and prevented the bis-allylic hydroperoxide of 20:3n-3 but not 20:2n-6 to interact with the catalytic metal. The oxidized form, Mn(III)-LOX, likely accepts an electron from the bis-allylic hydroperoxide anion with the formation of the peroxyl radical, but rearrangement of 11-hydroperoxyoctadecatrienoic acid by Mn-LOX was not reduced in D(2)O (pD 7.5), and aqueous Fe(3+) did not transfer 11S-hydroperoxy-9Z,12Z,15Z-octadecatrienoic acid to allylic hydroperoxides. Mutants in the vicinity of the catalytic metal, Asn466Leu and Ser469Ala, had little influence on bis-allylic hydroperoxide rearrangement. In conclusion, Mn-LOX transforms bis-allylic hydroperoxides to allylic by a reaction likely based on the positioning of the hydroperoxide close to Mn(3+) and electron transfer to the metal, with the formation of a bis-allylic peroxyl radical, beta-fragmentation, and oxygenation under steric control by the protein.

Acyclic 1,4-Stereocontrol via Reductive 1,3-Transpositions

One-pot reduction/allylic diazene rearrangement of lactic acid- and mandelic acid-derived alpha,beta-unsaturated tosyl hydrazones leads to 1,4-syn- or 1,4-anti-E-2-alkenyl arrays in high yield and diastereoselectivity. Either the syn or the anti diastereomer can be prepared by choosing the appropriate alkene stereoisomer of the hydrazone. The E-alkenes led to the 1,4-syn isomers, while the Z-alkenes led to the 1,4-anti isomers, both with > or =20:1 diastereoselectivity.

A graftable LDV peptidomimetic: Design, synthesis and application to a blood filtration membrane

A graftable LDV (Leu-Asp-Val) peptidomimetic molecule (B-c) has been prepared from 3-(5-amino-2-hydroxy)phenyl-propionic acid, as alpha(4)beta(1) (VLA-4) integrin ligand. For that purpose, the mechanism of 3-(4-azidophenyl)propionic acid rearrangement has been revisited. Activation of Durapore DVPP-hydrophilic membrane, by surface wet chemistry using triazine trifluoride, followed by covalent coupling of B-c produced a modified filter (0.8% of derivatisation from XPS analysis) with improved capacity of leukocyte retention.

Probing nucleation, reverse annealing, and chaperone function along the reaction path of HIV-1 single-strand transfer

Reverse transcription of the HIV-1 genome involves several nucleic acid rearrangement steps that are catalyzed (chaperoned) by the nucleocapsid protein (NC), including the annealing of the transactivation response region (TAR) RNA of the genome to the complementary sequence (TAR DNA) in minus-strand strong-stop DNA. It has been extremely challenging to obtain unambiguous mechanistic details on the annealing process at the molecular level because of the kinetic involvement of a complex and heterogeneous set of nucleic acid/protein complexes of variable structure and variable composition. Here, we investigate the in vitro annealing mechanism using a multistep single-molecule spectroscopy kinetic method. In this approach, an immobilized hairpin is exposed to a multistep programmed concentration sequence of NC, model complementary targeted-oligonucleotides, and buffer-only solutions. The sequence controllably "drags" single immobilized TAR hairpins among the kinetic stable states of the reaction mechanism; i.e., reactants, intermediates, and products. This single-molecule spectroscopy method directly probes kinetic reversibility and the chaperone (catalytic) role of NC at various stages along the reaction sequence, giving access to previously inaccessible kinetic processes and rate constants. By employing target oligonucleotides for specific TAR regions, we kinetically trap and investigate structural models for putative nucleation complexes for the annealing process. The new results lead to a more complete and detailed understanding of the ability of NC to promote nucleic acid/nucleic acid rearrangement processes. This includes information on the ability of NC to chaperone "reverse annealing" in single-strand transfer and the first observation of partially annealed, conformational substates in the annealing mechanism.

Insights on the role of nucleic acid/protein interactions in chaperoned nucleic acid rearrangements of HIV-1 reverse transcription

HIV-1 reverse transcription requires several nucleic acid rearrangement steps that are "chaperoned" by the nucleocapsid protein (NC), including minus-strand transfer, in which the DNA transactivation response element (TAR) is annealed to the complementary TAR RNA region of the viral genome. These various rearrangement processes occur in NC bound complexes of specific RNA and DNA structures. A major barrier to the investigation of these processes in vitro has been the diversity and heterogeneity of the observed nucleic acid/protein assemblies, ranging from small complexes of only one or two nucleic acid molecules all the way up to large-scale aggregates comprised of thousands of NC and nucleic acid molecules. Herein, we use a flow chamber approach involving rapid NC/nucleic acid mixing to substantially control aggregation for the NC chaperoned irreversible annealing kinetics of a model TAR DNA hairpin sequence to the complementary TAR RNA hairpin, i.e., to form an extended duplex. By combining the flow chamber approach with a broad array of fluorescence single-molecule spectroscopy (SMS) tools (FRET, molecule counting, and correlation spectroscopy), we have unraveled the complex, heterogeneous kinetics that occur during the course of annealing. The SMS results demonstrate that the TAR hairpin reactant is predominantly a single hairpin coated by multiple NCs with a dynamic secondary structure, involving equilibrium between a "Y" shaped conformation and a closed one. The data further indicate that the nucleation of annealing occurs in an encounter complex that is formed by two hairpins with one or both of the hairpins in the "Y" conformation.

Combined Cyclic Vomiting and Kearns-Sayre Syndromes

The third case of cyclic vomiting syndrome with a large mitochondrial deoxyribonucleic acid rearrangement is described. Multiple neuromuscular anomalies are present that meet the diagnostic criteria for Kearns-Sayre syndrome, as well as severe symmetrical growth retardation. A 3-kilobase mitochondrial deoxyribonucleic acid deletion (nucleotides 10970-14118) was found at 30-40% heteroplasmy in the blood of the child, but not the mother. Although mitochondrial dysfunction and disease-associated mitochondrial deoxyribonucleic acid sequence variants are believed to be present in most cyclic vomiting syndrome cases, these variants are rarely identifiable on "standard" mitochondrial deoxyribonucleic acid testing. However, finding a rearrangement has clinical implications, and standard testing is recommended in those cyclic vomiting syndrome cases with neuromuscular disease and/or growth retardation, whether maternal inheritance is present or not.

Reactions of d-fructose in water at temperatures up to 400 °C and pressures up to 100 MPa

Reactions of d-fructose in water at high temperatures (350 and 400 °C) and pressures (up to 100 MPa) were studied using a flow reactor. High temperature (400 °C) and moderate pressure (40 MPa) conditions enhanced the yields of retro-aldol related products such as glyceraldehyde, dihydroxyacetone and pyruvaldehyde. High temperature, high pressure conditions enhanced retro-aldol reactions and water related reactions such as hydrolysis and dehydration. Comparison between d-fructose and d-glucose experiments showed that higher yields for 5-HMF were obtained starting from d-fructose than d-glucose. Surprisingly, higher yields of furfural were obtained starting from d-glucose than from d-fructose which is contrary to reaction pathways in the hydrothermal literature. Based on the experimental results, a possible reaction scheme is proposed for water catalyzed (i) benzilic acid rearrangement reactions from pyruvaldehyde to lactic acid and (ii) retro-aldol reaction from d-glucose to furfural.

Modelling of morphology and proton transport in PFSA membranes

Computational modelling studies of the structure of perfluorosulfonic acid (PFSA) ionomer membranes consistently exhibit a nanoscopic phase-separated morphology in which the ionic side chains and aqueous counterions segregate from the fluorocarbon backbone to form clusters or channels. Although these investigations do not unambiguously predict the size or shape of the clusters, and whether or not the channels percolate the matrix or if the connections between them are more transient, the sequence of co-monomers along the main chain appears strongly to influence the domain size of the ionic regions, with more blocky sequences giving rise to larger domain sizes. The fundamental insight that substantial rearrangement of the sulfonic acid terminated side chains and fluorocarbon backbone takes place during swelling or shrinkage is borne out by both molecular and mesoscale simulations of model PFSA polymers, along with ab initio electronic structure calculations of minimally hydrated oligomeric fragments. Molecular-level modelling of proton transport in PFSA membranes attests to the complexity of the underlying mechanisms and the need to examine the chemical and physical processes at several distinct time and length scales. These investigations have revealed that the conformation of the fluorocarbon backbone, flexibility of the sidechains, and degree of aggregation and association of the sulfonic acid groups under minimally hydrated conditions collectively control the dissociation of the protons and the formation of Zundel and Eigen cations. The former appear to be the dominant charge carriers when the limiting water content allows only for the formation of a contact ion pair with the tethered sulfonate anion. As the water content increases, solvent-separated Eigen ions begin to appear, indicating that the dominant mechanism for diffusion of protons occurs over a region approximately 4 A away from the sulfonate groups. Finally, both the vehicular and Grotthuss shuttling mechanisms contribute to the mobility of the protons but, surprisingly, they are not always correlated, resulting in a lower overall diffusion coefficient. In summary, as the preceding observations indicate, the state of computational modelling of PFSA membranes has progressed sufficiently over the last decade to enable its use as a powerful predictive tool with which to guide the process of designing novel membrane materials for fuel cell applications.

Regiospecific Synthesis of Benzo[b]fluorenones via Ring Contraction by Benzil—Benzilic Acid Rearrangement of Benz[a]anthracene‐5,6‐diones.

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Efficient N-Heterocyclic Carbene-Catalyzed O- to C-Acyl Transfer

[reaction: see text] An N-heterocyclic carbene promotes the rearrangement of alpha-amino acid derived O-acyl carbonates to their corresponding C-acylated isomers, generating a C-C bond and a quaternary stereocenter with high efficiency, under mild reaction conditions and with low catalyst loadings.

Regiospecific Synthesis of Benzo[b]fluorenones via Ring Contraction by Benzil-Benzilic Acid Rearrangement of Benz[a]anthracene-5,6-diones

A regiospecific route to benzo[b]fluorenones is described. The synthesis is based upon a one-pot, regiospecific benzannulation of 1,4-dipolar synthons with naphthoquinone monoketal and ring contraction of the generated benz[a]anthracene-5,6-diones through benzil-benzilic acid rearrangement.

A FMO-Controlled Reaction Path in the Benzil−Benzilic Acid Rearrangement

Reaction paths for the title rearrangement along with its methyl analogue were investigated by density functional theory calculations. The reaction model is R-CO-CO-R + OH(-)(H2O)4 --> R2C(OH)-COO- + (H2O)4 (R = Me and Ph), where the water tetramer is employed both for solvation to OH- and for the proton relay along hydrogen bonds. The reaction is composed of OH- addition, C-C rotation, carbanion [1,2] migration, and proton relay toward the product anions. The rate-determining step was calculated to be the carbanion migration. Apparently, carbanion [1,2] migration is unlikely relative to the carbonium ion one. However, LUMOs of the 1,2-diketones have large and nodeless lobes at the reaction center, the C1-C2 bond. The specific LUMO character is reflected both in the [2+1]-like one-center nucleophilic addition and in the carbanion [1,2] shift. The proton relay involved in the isomerization from the oxo intermediate to the carboxylate was calculated to take place via the water tetramer.

Studies Directed toward the Synthesis of Terreulactone A: Rapid Construction of the A, B, C Rings

[structure: see text]. An efficient, rapid synthesis of the A, B, C rings of terreulactone A is described. Key steps in the synthesis include a diastereoselective benzylic acid rearrangement to create the desired quaternary center at C2 and a mild bromolactonization to assemble the lactonic ring A.

Conversion of Glycerin into Lactic Acid by Alkaline Hydrothermal Reaction

Abstract Hydrothermal decomposition experiments of glycerin with an alkali showed that glycerin could be converted into lactic acid with a high yield of about 90 mol % based on glycerin used. Discussion on the pathway for the conversion of glycerin to lactic acid suggests that glycerin is first decomposed to pyruvaldehyde with elimination of hydrogen by a H− shift to the adjacent hydrogen. Pyruvaldehyde formed is then converted into lactic acid ion by the benzilic acid rearrangement.

Sterically Biased 3,3-Sigmatropic Rearrangement of Azides: Efficient Preparation of Nonracemic α-Amino Acids and Heterocycles

[reaction: see text] Homochiral alpha-amino acids, heterocycles, and carbocycles are efficiently constructed via a short sequence of reactions starting from the chiral auxiliary p-menthane-3-carboxaldehyde. The key feature of the sequence is a highly selective tandem Mitsunobu/3,3-sigmatropic rearrangement of hydrazoic acid that procures enantiomerically enriched allylic azides. The sequence is either terminated by oxidative cleavage to provide amino acids or by ring-closing metathesis to provide heterocycles or carbocycles bearing nitrogen.

A New Approach to 1-Substituted-1,2Alkadienephosphonates I

The possibility of the substitution of the H atom at the C1-position of the phosphorylated allenes with different kind of electrophiles has been discussed and evidence for the mechanism of the heterocyclization of allenephosphonates by the reaction with electrophilic reagents has been supplied. The new approach for the synthesis of 1-substituted-1,2-alkadiene phosphonates via the acetylene-allene rearrangement of acetylenecarboxylic acid has been discussed.

Synthesis of a tetrasubstituted arylphosphonate via the anionic phospho-Fries rearrangement

The anionic phospho-Fries rearrangement of phosphoric acid (3,5-di-isopropoxy)phenyl ester diethyl ester ( 11 ) gave rise to (2-hydroxy-4,6-di-isopropoxy-phenyl)phosphonic acid diethyl ester ( 12 ) in excellent yield. The phenol functionality of 12 was converted to the corresponding triflate which was coupled with vinyltributylstannane, under Stille conditions, to give a styrene. This molecule is intended to serve as the aromatic fragment in the synthesis of a phosphorus-based transition-state analogue for the hydrolysis of the S-(−)-zearalenone lactone.

Short Communication: Rearrangement of Rumenic Acid in Ruminant Fats: A Marker of Thermal Treatment

Rumenic (cis-9,trans-11 18:2) acid is the main conjugated linoleic acid (CLA) isomer in milk and other ruminant fats. Anhydrous regular and high-CLA butterfats were heated at 200°C for 2, 4, and 6h under atmospheric conditions. [1,5] Sigmatropic isomerization of rumenic acid occurred, resulting in the formation of trans-8,cis-10 18:2 acid, as determined by mass spectrometry of its 4,4-dimethyloxazoline derivative. Rate of isomerization was monitored by gas-liquid chromatography, using a 120-m capillary column coated with 70% equivalent cyanoalkylpolysiloxane polymer, and reaction was of first order. Furthermore, [1,5] sigmatropic rearrangement product analysis can be used as an indicator of heat treatment of natural fats and oils containing CLA.

The Rearrangement of an Allylic Dithiocyanate: An Experiment for Organic or Physical Chemistry Using NMR Analysis

An experiment suitable for students who have taken either organic chemistry or organic and physical chemistry is described. The simple preparation and molecular rearrangement of thiocyanic acid, 2-methylene-1,3-propanediyl ester to 1-propene, (3-isothiocyanato-2-isothiocyanatomethyl) occurs readily in the temperature range of 65–90°C and progress of the reaction is readily tracked by proton NMR. The buildup and decline of the intermediate, thiocyanic acid, 2-(isothiocyanatomethyl)-2-propenyl ester, is readily seen. Start and stop methods for conducting the reaction in simple apparatus external to the NMR instrument are described thus making the experiment suitable for several students to do in a limited period of time without tying up the NMR for long periods. A controlled temperature probe for the NMR instrument is not needed. Advanced students can determine rate constants for the reactions, compute activation parameters, and observe solvent effects.

Tunneling effects of dyadic prototropic rearrangement of hypophosphorous acid

The structures and energies of the tautomeric forms of hypophosphorous acid and phosphine oxide were calculated by DFT. The tautomeric forms are in equilibrium, and intramolecular hydrogen bonding is shown to be possible in both tautomeric forms of phthalimidophosphorous acid. The equilibrium constants are estimated within a wide temperature range. The necessity to take into account the tunneling contribution to the rate constant of the rearrangement is demonstrated.