Epoxidation of Alpha-Methylstyrene and its Lewis Acid Rearrangement to 2-Phenylpropanal

NASA Astrophysics Data System (ADS)

Garin, David L.; Gamber, Melissa; Rowe, Bradley J.

1996-06-01

This undergraduate organic lab experiment includes procedures for the peracid epoxidation of an olefin and the Lewis acid rearrangement of an epoxide to a carbonyl compound. Product mixtures and transformations can be readily analyzed by several spectroscopic techniques.

Acid-Catalyzed Preparation of Biodiesel from Waste Vegetable Oil: An Experiment for the Undergraduate Organic Chemistry Laboratory

ERIC Educational Resources Information Center

Bladt, Don; Murray, Steve; Gitch, Brittany; Trout, Haylee; Liberko, Charles

2011-01-01

This undergraduate organic laboratory exercise involves the sulfuric acid-catalyzed conversion of waste vegetable oil into biodiesel. The acid-catalyzed method, although inherently slower than the base-catalyzed methods, does not suffer from the loss of product or the creation of emulsion producing soap that plagues the base-catalyzed methods when…

An Efficient Synthesis of de novo Imidates via Aza-Claisen Rearrangements of N-Allyl Ynamides

PubMed Central

DeKorver, Kyle A.; North, Troy D.; Hsung, Richard P.

2010-01-01

A novel thermal 3-aza-Claisen rearrangement of N-allyl ynamides for the synthesis of α-allyl imidates is described. Also, a sequential aza-Claisen, Pd-catalyzed Overman rearrangement is described for the synthesis of azapine-2-ones. PMID:21278848

Efficient production of free fatty acids from ionic liquid-based acid- or enzyme-catalyzed bamboo hydrolysate.

PubMed

Mi, Le; Qin, Dandan; Cheng, Jie; Wang, Dan; Li, Sha; Wei, Xuetuan

2017-03-01

Two engineered Escherichia coli strains, DQ101 (MG1655 fadD - )/pDQTES and DQ101 (MG1655 fadD - )/pDQTESZ were constructed to investigate the free fatty acid production using ionic liquid-based acid- or enzyme-catalyzed bamboo hydrolysate as carbon source in this study. The plasmid, pDQTES, carrying an acyl-ACP thioesterase 'TesA of E. coli in pTrc99A was constructed firstly, and then (3R)-hydroxyacyl-ACP dehydratase was ligated after the TesA to give the plasmid pDQTESZ. These two strains exhibited efficient fatty acid production when glucose was used as the sole carbon source, with a final concentration of 2.45 and 3.32 g/L, respectively. The free fatty acid production of the two strains on xylose is not as efficient as that on glucose, which was 2.32 and 2.96 g/L, respectively. For mixed sugars, DQ101 (MG1655 fadD - )-based strains utilized glucose and pentose sequentially under the carbon catabolite repression (CCR) regulation. The highest total FFAs concentration from the mixed sugar culture reached 2.81 g/L by DQ101 (MG1655 fadD - )/pDQTESZ. Furthermore, when ionic liquid-based enzyme-catalyzed bamboo hydrolysate was used as the carbon source, the strain DQ101 (MG1655 fadD - )/pDQTESZ could produce 1.23 g/L FFAs with a yield of 0.13 g/g, and while it just produced 0.65 g/L free fatty acid with the ionic liquid-based acid-catalyzed bamboo hydrolysate as the feedstock. The results suggested that enzymatic catalyzed bamboo hydrolysate with ionic liquid pretreatment could serve as an efficient feedstock for free fatty acid production.

Degradation of Perfluorooctanoic Acid and Perfluoroctane Sulfonate by Enzyme Catalyzed Oxidative Humification Reactions

NASA Astrophysics Data System (ADS)

Huang, Q.

2016-12-01

Poly- and perfluoroalkyl substances (PFASs) are alkyl based chemicals having multiple or all hydrogens replaced by fluorine atoms, and thus exhibit high thermal and chemical stability and other unusual characteristics. PFASs have been widely used in a wide variety of industrial and consumer products, and tend to be environmentally persistent. Perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS) are two representative PFASs that have drawn particular attention because of their ubiquitous presence in the environment, resistance to degradation and toxicity to animals. This study examined the decomposition of PFOA and PFOS in enzyme catalyzed oxidative humification reactions (ECOHR), a class of reactions that are ubiquitous in the environment involved in natural organic humification. Reaction rates and influential factors were examined, and high-resolution mass spectrometry was used to identify possible products. Fluorides and partially fluorinated compounds were identified as likely products from PFOA and PFOS degradation, which were possibly formed via a combination of free radical decomposition, rearrangements and coupling processes. The findings suggest that PFOA and PFOS may be transformed during humification, and ECOHR can potentially be used for the remediation of these chemicals.

A tandem cross-metathesis/semipinacol rearrangement reaction.

PubMed

Plummer, Christopher W; Soheili, Arash; Leighton, James L

2012-05-18

An efficient and (E)-selective synthesis of a 6-alkylidenebicyclo[3.2.1]octan-8-one has been developed. The key step is a tandem cross-metathesis/semipinacol rearrangement reaction, wherein the Hoveyda-Grubbs II catalyst, or more likely a derivative thereof, serves as the Lewis acid for the rearrangement. Despite the fact that both the starting alkene and the cross-metathesis product are viable rearrangement substrates, only the latter rearranges, suggesting that the Lewis acidic species is generated only after the cross-metathesis reaction is complete.

Approaches to α-amino acids via rearrangement to electron-deficient nitrogen: Beckmann and Hofmann rearrangements of appropriate carboxyl-protected substrates

PubMed Central

Rao, V Mohana

2012-01-01

Summary The titled approaches were effected with various 2-substituted benzoylacetic acid oximes 3 (Beckmann) and 2-substituted malonamic acids 9 (Hofmann), their carboxyl groups being masked as a 2,4,10-trioxaadamantane unit (an orthoacetate). The oxime mesylates have been rearranged with basic Al2O3 in refluxing CHCl3, and the malonamic acids with phenyliodoso acetate and KOH/MeOH. Both routes are characterized by excellent overall yields. Structure confirmation of final products was conducted with X-ray diffraction in selected cases. The final N-benzoyl and N-(methoxycarbonyl) products are α-amino acids with both carboxyl and amino protection; hence, they are of great interest in peptide synthesis. PMID:23019476

Synthesis of (±)-amathaspiramide F and discovery of an unusual stereocontrolling element for the [2,3]-Stevens rearrangement.

PubMed

Soheili, Arash; Tambar, Uttam K

2013-10-04

A formal total synthesis of (±)-amathaspiramide F through a tandem palladium-catalyzed allylic amination/[2,3]-Stevens rearrangement is reported. The unexpected diastereoselectivity of the [2,3]-Stevens rearrangement was controlled by the substitution patterns of an aromatic ring. This discovery represents a new stereocontrolling element for [2,3]-sigmatropic rearrangements in complex molecular settings.

Lewis super-acid catalyzed cyclizations: a new route to fragrance compounds.

PubMed

Coulombel, Lydie; Grau, Fanny; Weïwer, Michel; Favier, Isabelle; Chaminade, Xavier; Heumann, Andreas; Bayón, J Carles; Aguirre, Pedro A; Duñach, Elisabet

2008-06-01

This review deals with the application of Lewis super acids such as Al(III), In(III), and Sn(IV) triflates and triflimidates as catalysts in the synthesis of fragrance materials. Novel catalytic reactions involving C-C and C-heteroatom bond-forming reactions, as well as cycloisomerization processes are presented. In particular, Sn(IV) and Al(III) triflates were employed as catalysts in the selective cyclization of unsaturated alcohols to cyclic ethers, as well as in the cyclization of unsaturated carboxylic acids to lactones. The addition of thiols and thioacids to non-activated olefins, both in intra- and intermolecular versions, was efficiently catalyzed by In(III) derivatives. Sn(IV) Triflimidates catalyzed the cycloisomerization of highly substituted 1,6-dienes to gem-dimethyl-substituted cyclohexanes bearing an isopropylidene substituent. The hydroformylation of these unsaturated substrates, catalyzed by a Rh(I) complex with a bulky phosphite ligand, selectively afforded the corresponding linear aldehydes. The olfactory evaluation of selected heterocycles, carbocycles, and aldehydes synthesized is also discussed.

Gold-Catalyzed Formal C-C Bond Insertion Reaction of 2-Aryl-2-diazoesters with 1,3-Diketones.

PubMed

Ren, Yuan-Yuan; Chen, Mo; Li, Ke; Zhu, Shou-Fei

2018-06-29

The transition-metal-catalyzed formal C-C bond insertion reaction of diazo compounds with monocarbonyl compounds is well established, but the related reaction of 1,3-diketones instead gives C-H bond insertion products. Herein, we report a protocol for a gold-catalyzed formal C-C bond insertion reaction of 2-aryl-2-diazoesters with 1,3-diketones, which provides efficient access to polycarbonyl compounds with an all-carbon quaternary center. The aryl ester moiety plays a crucial role in the unusual chemoselectivity, and the addition of a Brønsted acid to the reaction mixture improves the yield of the C-C bond insertion product. A reaction mechanism involving cyclopropanation of a gold carbenoid with an enolate and ring-opening of the resulting donor-acceptor-type cyclopropane intermediate is proposed. This mechanism differs from that of the traditional Lewis-acid-catalyzed C-C bond insertion reaction of diazo compounds with monocarbonyl compounds, which involves a rearrangement of a zwitterion intermediate as a key step. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ring Expansion and Rearrangements of Rhodium(II) Azavinyl Carbenes

PubMed Central

Selander, Nicklas; Worrell, Brady T.

2013-01-01

An efficient, regioselective and convergent method for the ring expansion and rearrangement of 1-sulfonyl-1,2,3-triazoles under rhodium(II)-catalyzed conditions is described. These denitrogenative reactions form substituted enaminone and olefin-based products, which in the former case can be further functionalized to unique products rendering the sulfonyl triazole traceless. PMID:23161725

Catalytic and Thermal 1,2-Rearrangement of (α-Mercaptobenzyl)trimethylsilane

NASA Astrophysics Data System (ADS)

Zhang, Jie; Cui, Mengzhong; Feng, Shengyu; Sun, Xiaomin; Feng, Dacheng

2009-09-01

The mechanisms of catalytic and thermal 1,2-rearrangement of (α-mercaptobenzyl)trimethylsilane were studied by using density functional theory (DFT) at the MP2/6-31+G(d,p)//B3LYP/6-31G(d) levels. The results show that (α-mercaptobenzyl)trimethylsilane rearranges to (benzylthio)trimethylsilane through a trimethylsilyl group migration from C to S atom via a transition state of pentacoordinate Si atom with or without radical initiators. The low reaction activation energy (15.1 kcal/mol) is responsible for the fast rearrangement in the presence of radical initiators. Both radical and nonradical thermal rearrangement mechanisms were suggested, and the radical mechanism dominates through its self-catalyzing. These results are consistent with the experiment results. The activation energy (ΔHact = 15.1 kcal/mol) for the rate-determining step within the self-catalytic cycle is low enough to make (trimethylsilylbenzyl)thiyl radical be a reasonable catalyst for the thermal rearrangement. The catalytic and thermal 1,2-rearrangement mechanisms of (α-mercaptobenzyl)trimethylsilane, especially the self-catalytic radical mechanism, were revealed for the first time. The comparison of the rearrangement mechanisms between (α-mercaptobenzyl)trimethylsilane and silylmethanethiol discloses the factors in determining the reaction mechanism of such kinds of mercaptoalkyl-functionalized organosilanes. The phenyl group is found to be favorable for the radical rearrangement, thus making (α-mercaptobenzyl)trimethylsilane instable.

Synthesis of Rosin Acid Starch Catalyzed by Lipase

PubMed Central

Lin, Rihui; Li, He; Long, Han; Su, Jiating; Huang, Wenqin

2014-01-01

Rosin, an abundant raw material from pine trees, was used as a starting material directly for the synthesis of rosin acid starch. The esterification reaction was catalyzed by lipase (Novozym 435) under mild conditions. Based on single factor experimentation, the optimal esterification conditions were obtained as follows: rosin acid/anhydrous glucose unit in the molar ratio 2 : 1, reaction time 4 h at 45°C, and 15% of lipase dosage. The degree of substitution (DS) reaches 0.098. Product from esterification of cassava starch with rosin acid was confirmed by FTIR spectroscopy and iodine coloration analysis. Scanning electron microscopy and X-ray diffraction analysis showed that the morphology and crystallinity of the cassava starch were largely destroyed. Thermogravimetric analysis indicated that thermal stability of rosin acid starch decreased compared with native starch. PMID:24977156

Acetic Acid Can Catalyze Succinimide Formation from Aspartic Acid Residues by a Concerted Bond Reorganization Mechanism: A Computational Study

PubMed Central

Takahashi, Ohgi; Kirikoshi, Ryota; Manabe, Noriyoshi

2015-01-01

Succinimide formation from aspartic acid (Asp) residues is a concern in the formulation of protein drugs. Based on density functional theory calculations using Ace-Asp-Nme (Ace = acetyl, Nme = NHMe) as a model compound, we propose the possibility that acetic acid (AA), which is often used in protein drug formulation for mildly acidic buffer solutions, catalyzes the succinimide formation from Asp residues by acting as a proton-transfer mediator. The proposed mechanism comprises two steps: cyclization (intramolecular addition) to form a gem-diol tetrahedral intermediate and dehydration of the intermediate. Both steps are catalyzed by an AA molecule, and the first step was predicted to be rate-determining. The cyclization results from a bond formation between the amide nitrogen on the C-terminal side and the side-chain carboxyl carbon, which is part of an extensive bond reorganization (formation and breaking of single bonds and the interchange of single and double bonds) occurring concertedly in a cyclic structure formed by the amide NH bond, the AA molecule and the side-chain C=O group and involving a double proton transfer. The second step also involves an AA-mediated bond reorganization. Carboxylic acids other than AA are also expected to catalyze the succinimide formation by a similar mechanism. PMID:25588215

Acetic acid can catalyze succinimide formation from aspartic acid residues by a concerted bond reorganization mechanism: a computational study.

PubMed

Takahashi, Ohgi; Kirikoshi, Ryota; Manabe, Noriyoshi

2015-01-12

Succinimide formation from aspartic acid (Asp) residues is a concern in the formulation of protein drugs. Based on density functional theory calculations using Ace-Asp-Nme (Ace = acetyl, Nme = NHMe) as a model compound, we propose the possibility that acetic acid (AA), which is often used in protein drug formulation for mildly acidic buffer solutions, catalyzes the succinimide formation from Asp residues by acting as a proton-transfer mediator. The proposed mechanism comprises two steps: cyclization (intramolecular addition) to form a gem-diol tetrahedral intermediate and dehydration of the intermediate. Both steps are catalyzed by an AA molecule, and the first step was predicted to be rate-determining. The cyclization results from a bond formation between the amide nitrogen on the C-terminal side and the side-chain carboxyl carbon, which is part of an extensive bond reorganization (formation and breaking of single bonds and the interchange of single and double bonds) occurring concertedly in a cyclic structure formed by the amide NH bond, the AA molecule and the side-chain C=O group and involving a double proton transfer. The second step also involves an AA-mediated bond reorganization. Carboxylic acids other than AA are also expected to catalyze the succinimide formation by a similar mechanism.

Development of melamine modified urea formaldehyde resins based o nstrong acidic pH catalyzed urea formaldehyde polymer

Treesearch

Chung-Yun Hse

2009-01-01

To upgrade the performance of urea-formaldehyde (UF) resin bonded particleboards, melamine modified urea-formaldehyde (MUF) resins based on strong acidic pH catalyzed UF polymers were investigated. The study was conducted in a series of two experiments: 1) formulation of MUF resins based on a UF polymer catalyzed with strong acidic pH and 2) determination of the...

The Lewis-acid-catalyzed synthesis of hyperbranched poly(glycerol-diacid)s in toluene

USDA-ARS?s Scientific Manuscript database

The first examples of monomeric glycerol-derived hyperbranched polyesters produced in a non-polar solvent system are reported here. The polymers were made by the Lewis acid (dibutyltin(IV)oxide)-catalyzed polycondensation of glycerol with either succinic acid (n (aliphatic chain length)=2), glutari...

Chiral Brønsted Acid-Catalyzed Allylboration of Aldehydes

PubMed Central

Jain, Pankaj; Antilla, Jon C.

2010-01-01

The catalytic enantioselective allylation of aldehydes is a long-standing problem with considerable interest to the chemical community. We wish to disclose a new high yielding and highly enantioselective chiral Brønsted acid-catalyzed allylboration of aldehydes. The reaction is shown to be highly general, with broad substrate scope that covers aryl, heteroaryl, α,β-unsaturated, and aliphatic aldehydes. The reaction conditions were also shown to be effective for the catalytic enantioselective crotylation of aldehydes. We believe that the high reactivity of the allyl boronate is due to protonation of the boronate oxygen by the chiral phosphoric acid catalyst. PMID:20690662

Enantioselective photochemistry via Lewis acid catalyzed triplet energy transfer

PubMed Central

Blum, Travis R.; Miller, Zachary D.; Bates, Desiree M.; Guzei, Ilia A.; Yoon, Tehshik P.

2017-01-01

Relatively few catalytic systems are able to control the stereochemistry of electronically excited organic intermediates. Here we report the discovery that a chiral Lewis acid complex can catalyze triplet energy transfer from an electronically excited photosensitizer. This strategy is applied to asymmetric [2+2] photocycloadditions of 2′-hydroxychalcones using tris(bipyridyl) ruthenium(II) as a sensitizer. A variety of electrochemical, computational, and spectroscopic data rule out substrate activation via photoinduced electron transfer and instead support a mechanism in which Lewis acid coordination dramatically lowers the triplet energy of the chalcone substrate. We expect that this approach will enable chemists to more broadly apply their detailed understanding of chiral Lewis acid catalysis to stereocontrol in reactions of electronically excited states. PMID:27980203

Chemistry of Amadori rearrangement products: analysis, synthesis, kinetics, reactions, and spectroscopic properties.

PubMed

Yaylayan, V A; Huyghues-Despointes, A

1994-01-01

The chemistry of the key intermediate in the Maillard reaction, the Amadori rearrangements product, is reviewed covering the areas of synthesis, chromatographic analyses, chemical and spectroscopic methods of characterization, reactions, and kinetics. Synthetic strategies involving free and protected sugars are described in detail with specific synthetic procedures. GC- and HPLC-based separations of Amadori products are discussed in relation to the type of columns employed and methods of detection. Applications of infrared (IR) and nuclear magnetic resonance (NMR) spectroscopy for structural elucidation of Amadori products are also reviewed. In addition, mass spectrometry of free, protected, and protein-bound Amadori products under different ionization conditions are presented. The mechanism of acid/base catalyzed thermal degradation reactions of Amadori compounds, as well as their kinetics of formation, are critically evaluated.

Highly efficient chemical process to convert mucic acid into adipic acid and DFT studies of the mechanism of the rhenium-catalyzed deoxydehydration.

PubMed

Li, Xiukai; Wu, Di; Lu, Ting; Yi, Guangshun; Su, Haibin; Zhang, Yugen

2014-04-14

The production of bulk chemicals and fuels from renewable bio-based feedstocks is of significant importance for the sustainability of human society. Adipic acid, as one of the most-demanded drop-in chemicals from a bioresource, is used primarily for the large-volume production of nylon-6,6 polyamide. It is highly desirable to develop sustainable and environmentally friendly processes for the production of adipic acid from renewable feedstocks. However, currently there is no suitable bio-adipic acid synthesis process. Demonstrated herein is the highly efficient synthetic protocol for the conversion of mucic acid into adipic acid through the oxorhenium-complex-catalyzed deoxydehydration (DODH) reaction and subsequent Pt/C-catalyzed transfer hydrogenation. Quantitative yields (99 %) were achieved for the conversion of mucic acid into muconic acid and adipic acid either in separate sequences or in a one-step process. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Catalysis of concerted reactions by antibodies: the Claisen rearrangement.

PubMed Central

Hilvert, D; Carpenter, S H; Nared, K D; Auditor, M T

1988-01-01

Monoclonal antibodies were prepared against a transition state analog inhibitor of chorismate mutase (EC 5.4.99.5). One of the antibodies catalyzes the rearrangement of chorismate to prephenate with rate accelerations of more than 2 orders of magnitude compared to the uncatalyzed reaction. Saturation kinetics were observed, and at 25 degrees C the values of kcat and Km were 1.2 X 10(-3) s-1 and 5.1 X 10(-5) M respectively. The transition state analog was shown to be a competitive inhibitor of the reaction with Ki equal to 0.6 microM. These results demonstrate the feasibility of using rationally designed immunogens to generate antibodies that catalyze concerted reactions. PMID:3393525

Sequential Diels–Alder/[3,3]-sigmatropic rearrangement reactions of β-nitrostyrene with 3-methyl-1,3-pentadiene

PubMed Central

Pipic, Alma; Zeller, Matthias; Tsetsakos, Panagiota

2013-01-01

Summary The tin(IV)-catalyzed reaction of β-nitrostyrene with (E)-3-methyl-1,3-pentadiene in toluene afforded two major nitronic ester cycloadducts in 27% and 29% yield that arise from the reaction at the less substituted diene double bond. Also present were four cycloadducts from the reaction at the higher substituted diene double bond, two of which were the formal cycloadducts of (Z)-3-methyl-1,3-pentadiene. A Friedel–Crafts alkylation product from the reaction of the diene, β-nitrostyrene, and toluene was also obtained in 10% yield. The tin(IV)-catalyzed reaction of β-nitrostyrene with (Z)-3-methyl-1,3-pentadiene in dichloromethane afforded four nitronic ester cycloadducts all derived from the reaction at the higher substituted double bond. One cycloadduct was isolated in 45% yield and two others are formal adducts of the E-isomer of the diene. The product formation in these reactions is consistent with a stepwise mechanism involving a zwitterionic intermediate. The initially isolated nitronic ester cycloadducts underwent tin(IV)-catalyzed interconversion, presumably via zwitterion intermediates. Cycloadducts derived from the reaction at the less substituted double bond of (E)-3-methyl-1,3-pentadiene underwent a [3,3]-sigmatropic rearrangement on heating to afford 4-nitrocyclohexenes. Cycloadducts derived from the reaction at the higher substituted diene double bond of either diene failed to undergo a thermal rearrangement. Rates and success of the rearrangement are consistent with a concerted mechanism possessing a dipolar transition state. An initial assessment of substituent effects on the rearrangement process is presented. PMID:24204426

Total synthesis of (+/-)-strychnine via a [4 + 2]-cycloaddition/rearrangement cascade.

PubMed

Zhang, Hongjun; Boonsombat, Jutatip; Padwa, Albert

2007-01-18

A new strategy for the synthesis of the Strychnos alkaloid (+/-)-strychnine has been developed and is based on an intramolecular [4 + 2]-cycloaddition/rearrangement cascade of an indolyl-substituted amidofuran. The critical D-ring was assembled by an intramolecular palladium-catalyzed enolate-driven cross-coupling of an N-tethered vinyl iodide. [reaction: see text].

The Ultrafast Wolff Rearrangement in the Gas Phase

NASA Astrophysics Data System (ADS)

Steinbacher, Andreas; Roeding, Sebastian; Brixner, Tobias; Nuernberger, Patrick

The Wolff rearrangement of gas-phase 5-diazo Meldrum's acid is disclosed with femtosecond ion spectroscopy. Distinct differences are found for 267 nm and 200 nm excitation, the latter leading to even two ultrafast rearrangement reactions.

Rh(III)-Catalyzed Decarboxylative Coupling of Acrylic Acids with Unsaturated Oxime Esters: Carboxylic Acids Serve as Traceless Activators

PubMed Central

2015-01-01

α,β-Unsaturated carboxylic acids undergo Rh(III)-catalyzed decarboxylative coupling with α,β-unsaturated O-pivaloyl oximes to provide substituted pyridines in good yield. The carboxylic acid, which is removed by decarboxylation, serves as a traceless activating group, giving 5-substituted pyridines with very high levels of regioselectivity. Mechanistic studies rule out a picolinic acid intermediate, and an isolable rhodium complex sheds further light on the reaction mechanism. PMID:24512241

Single-step synthesis of styryl phosphonic acids via palladium-catalyzed Heck coupling of vinyl phosphonic acid with aryl halides

DOE PAGES

McNichols, Brett W.; Koubek, Joshua T.; Sellinger, Alan

2017-10-27

Here, we have developed a single step palladium-catalyzed Heck coupling of aryl halides with vinyl phosphonic acid to produce functionalized (E)-styryl phosphonic acids. This pathway utilizes a variety of commercially available aryl halides, vinyl phosphonic acid and Pd(P(tBu) 3) 2 as catalyst. These conditions produce a wide range of styryl phosphonic acids with high purities and good to excellent yields (31–80%).

Single-step synthesis of styryl phosphonic acids via palladium-catalyzed Heck coupling of vinyl phosphonic acid with aryl halides

DOE Office of Scientific and Technical Information (OSTI.GOV)

McNichols, Brett W.; Koubek, Joshua T.; Sellinger, Alan

Here, we have developed a single step palladium-catalyzed Heck coupling of aryl halides with vinyl phosphonic acid to produce functionalized (E)-styryl phosphonic acids. This pathway utilizes a variety of commercially available aryl halides, vinyl phosphonic acid and Pd(P(tBu) 3) 2 as catalyst. These conditions produce a wide range of styryl phosphonic acids with high purities and good to excellent yields (31–80%).

Short communication: rearrangement of rumenic Acid in ruminant fats: a marker of thermal treatment.

PubMed

Destaillats, F; Japiot, C; Chouinard, P Y; Arul, J; Angers, P

2005-05-01

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 degrees C for 2, 4, and 6 h 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.

On the Brønsted acid-catalyzed homogeneous hydrolysis of furans.

PubMed

Nikbin, Nima; Caratzoulas, Stavros; Vlachos, Dionisios G

2013-11-01

Furan affairs: Electronic structure calculations of the homogeneous Brønsted acid-catalyzed hydrolysis of 2,5-dimethylfuran show that proton transfer to the β-position is rate-limiting and provides support that the hydrolysis follows general acid catalysis. By means of projected Fukui indices, we show this to be the case for unsubstituted, 2-, and 2,5-substituted furans with electron-donating groups. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Lipase-catalyzed synthesis of fattythioic acids from palm oil.

PubMed

Al-Mulla, Emad A Jaffar

2011-01-01

The present work focuses on the synthesis of fattythioic acids (FTAs) by a one-step lipase catalyzed reaction of palm oil with carbonothioic S,S-acid using Lipozyme. The product was characterized using Fourier transform infrared (FTIR) spectroscopy, proton nuclear magnetic resonance ((1)H NMR) technique and elemental analysis. The effects of various reaction parameters such as reaction time, temperature, amount of enzyme, molar ratio of substrates, and various organic solvents of the reaction system were investigated. The optimum conditions to produce FTAs were respectively, incubation time, 20 h, temperature, 40°C, amount of enzyme, 0.05 g and molar ratio of carbonothioic S,S-acid to palm oil, 5.0:1.0. Hexane was the best solvent for this reaction. The conversion of the products at optimum conditions was around 91%.

Acid-catalyzed rearrangements of flavan-4-phloroglucinol derivatives to novel 6-hydroxyphenyl-6a,llb-dihydro-6H-[1]benzofuro[2,3-c]-chromenes and hydroxyphenyl-3,2'-spirobi[dihydro[l]benzofurans

Treesearch

Petrus J. Steynberg; Jan P. Steynberg; Richard W. Hemingway; Daneel Ferreira; G. Wayne McGraw

1997-01-01

Acetic acid-catalyzed cleavage of proanthocyanidins in the presence of phloroglucinol gives a series of 2R procyanidin- and prodelphinidin-phloroglucinol adducts together with a novel 2S all-cis derivative implicating cleavage of the pyran ring and subsequent inversion of stereochernistry at C-2c. These flavan-4-phloroglucinol adducts also suffer dehydration to...

A comparative study of ozonation, iron coated zeolite catalyzed ozonation and granular activated carbon catalyzed ozonation of humic acid.

PubMed

Gümüş, Dilek; Akbal, Feryal

2017-05-01

This study compares ozonation (O 3 ), iron coated zeolite catalyzed ozonation (ICZ-O 3 ) and granular activated carbon catalyzed ozonation (GAC-O 3 ) for removal of humic acid from an aqueous solution. The results were evaluated by the removal of DOC that specifies organic matter, UV 254 absorbance, SUVA (Specific Ultraviolet Absorbance at 254 nm) and absorbance at 436 nm. When ozonation was used alone, DOC removal was 21.4% at an ozone concentration of 10 mg/L, pH 6.50 and oxidation time of 60 min. The results showed that the use of ICZ or GAC as a catalyst increased the decomposition of humic acid compared to ozonation alone. DOC removal efficiencies were 62% and 48.1% at pH 6.5, at a catalyst loading of 0.75 g/L, and oxidation time of 60 min for ICZ and GAC, respectively. The oxidation experiments were also carried out using <100 kDa and <50 kDa molecular size fractions of humic acid in the presence of ICZ or GAC. Catalytic ozonation also yielded better DOC and UV 254 reduction in both <50 kDa and <100 kDa fractions of HA compared to ozonation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Total Synthesis of (±)-Strychnine via a [4+2]-Cycloaddition/Rearrangement Cascade

PubMed Central

Zhang, Hongjun; Boonsombat, Jutatip

2008-01-01

A new strategy for the synthesis of the Strychnos alkaloid (±)-strychnine has been developed and is based on an intramolecular [4+2]-cycloaddition/rearrangement cascade of an indolyl substituted amidofuran. The critical D-ring was assembled by an intramolecular palladium catalyzed enolate-driven cross-coupling of an N-tethered vinyl iodide. PMID:17217284

Mechanism of α-ketol-type rearrangement of benzoin derivatives under basic conditions.

PubMed

Karino, Masahiro; Kubouchi, Daiki; Hamaoka, Kazuki; Umeyama, Shintaro; Yamataka, Hiroshi

2013-07-19

The mechanism of base-catalyzed rearrangement of ring-substituted benzoins in aqueous methanol was examined by kinetic and product analyses. Substituent effects on the rate and equilibrium constants revealed that the kinetic process has a different electron demand compared to the equilibrium process. Reactions in deuterated solvents showed that the rate of H/D exchange of the α-hydrogen is similar to the overall rate toward the equilibrium state. A proton-inventory experiment using partially deuterated solvents showed a linear dependence of the rate on the deuterium fraction of the solvent, indicating that only one deuterium isotope effect contributes to the overall rate process. All these results point to a mechanism in which the rearrangement is initiated by the rate-determining α-hydrogen abstraction rather than a mechanism with initial hydroxyl hydrogen abstraction as in the general α-ketol rearrangement.

N,N-Diethylurea-Catalyzed Amidation between Electron-Defficient Aryl Azides and Phenylacetaldehydes

PubMed Central

Xie, Sheng; Ramström, Olof; Yan, Mingdi

2015-01-01

Urea structures, of which N,N-diethylurea (DEU) proved to be the most efficient, were discovered to catalyze amidation reactions between electron-defficient aryl azides and phenylacetaldehydes. Experimental data support 1,3-dipolar cycloaddition between DEU-activated enols and electrophilic phenyl azides, especially perfluoroaryl azides, followed by rearrangement of the triazoline intermediate. The activation of the aldehyde under near-neutral conditions was of special importance in inhibiting dehydration/aromatization of the triazoline intermediate, thus promoting the rearrangement to form aryl amides. PMID:25616121

Bile acids at neutral and acidic pH induce apoptosis and gene cleavages in nasopharyngeal epithelial cells: implications in chromosome rearrangement.

PubMed

Tan, Sang-Nee; Sim, Sai-Peng

2018-04-12

Chronic rhinosinusitis (CRS) increases the risk of developing nasopharyngeal carcinoma (NPC) while nasopharyngeal reflux is known to be one of the major aetiological factors of CRS. Bile acid (BA), the component of gastric duodenal contents, has been recognised as a carcinogen. BA-induced apoptosis was suggested to be involved in human malignancies. Cells have the potential and tendency to survive apoptosis. However, cells that evade apoptosis upon erroneous DNA repair may carry chromosome rearrangements. Apoptotic nuclease, caspase-activated deoxyribonuclease (CAD) has been implicated in mediating translocation in leukaemia. We hypothesised that BA-induced apoptosis may cause chromosome breaks mediated by CAD leading to chromosome rearrangement in NPC. This study targeted the AF9 gene located at 9p22 because 9p22 is one of the most common deletion sites in NPC. We tested the ability of BA at neutral and acidic pH in inducing phosphatidylserine (PS) externalisation, reactive oxygen species (ROS) production, mitochondrial membrane potential (MMP) disruption, and caspase 3/7 activity in normal nasopharyngeal epithelial (NP69) and NPC (TWO4) cells. Inverse-PCR (IPCR) was employed to detect AF9 gene cleavages. To investigate the role of CAD in mediating these cleavages, caspase inhibition was performed. IPCR bands representing AF9 cleaved fragments were sequenced. BA-treated cells showed higher levels of PS externalisation, ROS production, MMP loss and caspase 3/7 activity than untreated control cells. The effect of BA in the induction of these intracellular events was enhanced by acid. BA at neutral and acidic pH also induced significant cleavage of the AF9 gene. These BA-induced gene cleavages were inhibited by Z-DEVD-FMK, a caspase-3 inhibitor. Intriguingly, a few chromosome breaks were identified within the AF9 region that was previously reported to participate in reciprocal translocation between the mixed lineage leukaemia (MLL) and AF9 genes in an acute

Copper-catalyzed formic acid synthesis from CO2 with hydrosilanes and H2O.

PubMed

Motokura, Ken; Kashiwame, Daiki; Miyaji, Akimitsu; Baba, Toshihide

2012-05-18

A copper-catalyzed formic acid synthesis from CO2 with hydrosilanes has been accomplished. The Cu(OAc)2·H2O-1,2-bis(diphenylphosphino)benzene system is highly effective for the formic acid synthesis under 1 atm of CO2. The TON value approached 8100 in 6 h. The reaction pathway was revealed by in situ NMR analysis and isotopic experiments.

Regioselective Copper-Catalyzed Amination of Chlorobenzoic Acids: Synthesis and Solid-State Structures of N-Aryl Anthranilic Acid Derivatives

PubMed Central

Mei, Xuefeng; August, Adam T.; Wolf, Christian

2008-01-01

A chemo- and regioselective copper-catalyzed cross-coupling reaction for effective amination of 2-chlorobenzoic acids with aniline derivatives has been developed. The method eliminates the need for acid protection and produces a wide range of N-aryl anthranilic acid derivatives in up to 99%. The amination was found to proceed with both electron-rich and electron-deficient aryl chlorides and anilines and also utilizes sterically hindered anilines such as 2,6-dimethylaniline and 2-tert-butylaniline. The conformational isomerism of appropriately substituted N-aryl anthranilic acids has been investigated in the solid state. Crystallographic analysis of seven anthranilic acid derivatives showed formation of two distinct supramolecular architectures exhibiting trans-anti- and unprecedented trans-syn-dimeric structures. PMID:16388629

Metabolism of 4-Chloronitrobenzene by the Yeast Rhodosporidium sp

PubMed Central

Corbett, Michael D.; Corbett, Bernadette R.

1981-01-01

The yeast Rhodosporidium sp. metabolized 4-chloronitrobenzene by a reductive pathway to give 4-chloroacetanilide and 4-chloro-2-hydroxyacetanilide as the major final metabolites. The intermediate production of 4-chloronitrosobenzene, 4-chlorophenylhydroxylamine, and 4-chloroaniline was demonstrated by high-pressure liquid chromatography. Additional studies with selected metabolites established that the metabolite 4-chloro-2-hydroxyacetanilide was produced by an initial Bamberger rearrangement of the hydroxylamine metabolite, followed by acetylation. Direct C hydroxylation of the aromatic ring was not observed in this species. No hydroxamic acid production was detected, even though significant concentrations of the nitroso and hydroxylamine precursors to this functional group were observed. PMID:16345757

Hydrogen-bonded intermediates and transition states during spontaneous and acid-catalyzed hydrolysis of the carcinogen (+)-anti-BPDE.

PubMed

Palenik, Mark C; Rodriguez, Jorge H

2014-07-07

Understanding mechanisms of (+)-anti-BPDE detoxification is crucial for combating its mutagenic and potent carcinogenic action. However, energetic-structural correlations of reaction intermediates and transition states during detoxification via hydrolysis are poorly understood. To gain mechanistic insight we have computationally characterized intermediate and transition species associated with spontaneous and general-acid catalyzed hydrolysis of (+)-anti-BPDE. We studied the role of cacodylic acid as a proton donor in the rate limiting step. The computed activation energy (ΔG‡) is in agreement with the experimental value for hydrolysis in a sodium cacodylate buffer. Both types of, spontaneous and acid catalyzed, BPDE hydrolysis can proceed through low-entropy hydrogen bonded intermediates prior to formation of transition states whose energies determine reaction activation barriers and rates.

Kinetic mechanism and structural requirements of the amine-catalyzed decarboxylation of oxaloacetic acid.

PubMed

Thalji, Nabil K; Crowe, William E; Waldrop, Grover L

2009-01-02

The kinetic and chemical mechanism of amine-catalyzed decarboxylation of oxaloacetic acid at pH 8.0 has been reevaluated using a new and versatile assay. Amine-catalyzed decarboxylation of oxaloacetic acid proceeds via the formation of an imine intermediate, followed by decarboxylation of the intermediate and hydrolysis to yield pyruvate. The decrease in oxaloacetic acid was coupled to NADH formation by malate dehydrogenase, which allowed the rates of both initial carbinolamine formation (as part of the imination step) and decarboxylation to be determined. By comparing the rates observed for a variety of amines and, in particular, diamines, the structural and electronic requirements for diamine-catalyzed decarboxylation at pH 8.0 were identified. At pH 8.0, monoamines were found to be very poor catalysts, whereas some diamines, most notably ethylenediamine, were excellent catalysts. The results indicate that the second amino group of diamines enhances the rate of imine formation by acting as a proton shuttle during the carbinolamine formation step, which enables diamines to overcome high levels of solvation that would otherwise inhibit carbinolamine, and thus imine, formation. The presence of the second amino group may also enhance the rate of the carbinolamine dehydration step. In contrast to the findings of previous reports, the second amino group participates in the reaction by enhancing the rate of decarboxylation via hydrogen-bonding to the imine nitrogen to either stabilize the negative charge that develops on the imine during decarboxylation or preferentially stabilize the reactive imine over the unreactive enamine tautomer. These results provide insight into the precise catalytic mechanism of several enzymes whose reactions are known to proceed via an imine intermediate.

Crystal structure of 2α-(1,1-di­phenyl­eth­yl)-4-methyl-4α,5α-diphenyl-1,3-dioxolane: the result of a non-acid pinacol rearrangement

PubMed Central

Kirchner, Richard M.; Corfield, Peter W. R.; Annabi, Michelle; Regan, John; Speina, Kevin; DiProperzio, Anthony; Ciaccio, James A.; Capitani, Joseph F.

2015-01-01

The title compound, C30H28O2, was obtained during recrystallization of (±)-1,2-diphenyl-1,2-propane­diol in 1-butanol, from an unexpected non-acid-catalyzed pinacol rearrangement followed by acetal formation of the newly formed aldehyde with the diol. The tri-substituted dioxolane ring has a twist conformation on the C—O bond opposite the methyl-substituted C atom. There is an intra­molecular C—H⋯π inter­action present involving one of the di­phenyl­ethyl rings and an H atom of the phenyl ring in position 4 of the dioxolane ring. In the crystal, mol­ecules are linked by weak C—H⋯O hydrogen bonds, forming chains along [001]. The chains are linked by a second C—H⋯π inter­action, forming sheets parallel to the bc plane. PMID:26594491

Chemoselective Nitro Group Reduction and Reductive Dechlorination Initiate Degradation of 2-Chloro-5-Nitrophenol by Ralstonia eutropha JMP134

PubMed Central

Schenzle, Andreas; Lenke, Hiltrud; Spain, Jim C.; Knackmuss, Hans-Joachim

1999-01-01

Ralstonia eutropha JMP134 utilizes 2-chloro-5-nitrophenol as a sole source of nitrogen, carbon, and energy. The initial steps for degradation of 2-chloro-5-nitrophenol are analogous to those of 3-nitrophenol degradation in R. eutropha JMP134. 2-Chloro-5-nitrophenol is initially reduced to 2-chloro-5-hydroxylaminophenol, which is subject to an enzymatic Bamberger rearrangement yielding 2-amino-5-chlorohydroquinone. The chlorine of 2-amino-5-chlorohydroquinone is removed by a reductive mechanism, and aminohydroquinone is formed. 2-Chloro-5-nitrophenol and 3-nitrophenol induce the expression of 3-nitrophenol nitroreductase, of 3-hydroxylaminophenol mutase, and of the dechlorinating activity. 3-Nitrophenol nitroreductase catalyzes chemoselective reduction of aromatic nitro groups to hydroxylamino groups in the presence of NADPH. 3-Nitrophenol nitroreductase is active with a variety of mono-, di-, and trinitroaromatic compounds, demonstrating a relaxed substrate specificity of the enzyme. Nitrosobenzene serves as a substrate for the enzyme and is converted faster than nitrobenzene. PMID:10347008

Lewis acid catalysis and ligand exchange in the asymmetric binaphthol-catalyzed propargylation of ketones.

PubMed

Grayson, Matthew N; Goodman, Jonathan M

2013-09-06

1,1'-Bi-2-naphthol (BINOL)-derived catalysts catalyze the asymmetric propargylation of ketones. Density functional theory (DFT) calculations show that the reaction proceeds via a closed six-membered transition structure (TS) in which the chiral catalyst undergoes an exchange process with the original cyclic boronate ligand. This leads to a Lewis acid type activation mode, not a Brønsted acid process, which accurately predicts the stereochemical outcome observed experimentally.

Chromosome-specific staining to detect genetic rearrangements

DOEpatents

Gray, Joe W.; Pinkel, Daniel; Tkachuk, Douglas; Westbrook, Carol

2013-04-09

Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyzes. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods and reagents are provided for the detection of genetic rearrangements. Probes and test kits are provided for use in detecting genetic rearrangements, particularly for use in tumor cytogenetics, in the detection of disease related loci, specifically cancer, such as chronic myelogenous leukemia (CML) and for biological dosimetry. Methods and reagents are described for cytogenetic research, for the differentiation of cytogenetically similar but genetically different diseases, and for many prognostic and diagnostic applications.

Grape skins (Vitis vinifera L.) catalyze the in vitro enzymatic hydroxylation of p-coumaric acid to caffeic acid.

PubMed

Arnous, Anis; Meyer, Anne S

2009-12-01

The ability of grape skins to catalyze in vitro conversion of p-coumaric acid to the more potent antioxidant caffeic acid was studied. Addition of different concentrations of p-coumaric to red grape skins (Cabernet Sauvignon) resulted in formation of caffeic acid. This caffeic acid formation (Y) correlated positively and linearly to p-coumaric acid consumption (X): Y = 0.5 X + 9.5; R (2) = 0.96, P < 0.0001. The kinetics of caffeic acid formation with time in response to initial p-coumaric acid levels and at different grape skin concentrations, indicated that the grape skins harboured an o-hydroxylation activity, proposedly a monophenol- or a flavonoid 3'-monooxygenase activity (EC 1.14.18.1 or EC 1.14.13.21). The K (m) of this crude o-hydroxylation activity in the red grape skin was 0.5 mM with p-coumaric acid.

Sequential aldol condensation-transition metal-catalyzed addition reactions of aldehydes, methyl ketones, and arylboronic acids.

PubMed

Liao, Yuan-Xi; Xing, Chun-Hui; Israel, Matthew; Hu, Qiao-Sheng

2011-04-15

Sequential aldol condensation of aldehydes with methyl ketones followed by transition metal-catalyzed addition reactions of arylboronic acids to form β-substituted ketones is described. By using the 1,1'-spirobiindane-7,7'-diol (SPINOL)-based phosphite, an asymmetric version of this type of sequential reaction, with up to 92% ee, was also realized. Our study provided an efficient method to access β-substituted ketones and might lead to the development of other sequential/tandem reactions with transition metal-catalyzed addition reactions as the key step. © 2011 American Chemical Society

Palladium-Catalyzed, Copper(I)-Mediated Coupling of Boronic Acids and Benzylthiocyanate. A Cyanide-Free Cyanation of Boronic Acids

PubMed Central

Zhang, Zhihui; Liebeskind, Lanny S.

2008-01-01

A new method for the synthesis of nitriles is described. As a complement to the classic cyanation of aryl halides using cyanide sources and a transition metal catalyst, the palladium-catalyzed cross-coupling of thiocyanates with boronic acids in the presence of copper(I) thiophene-2-carboxylate (CuTC) affords nitriles in good to excellent yields. PMID:16956219

Beckmann rearrangement within the ring C of oleanolic acid lactone: Synthesis, structural study and reaction mechanism analysis

NASA Astrophysics Data System (ADS)

Froelich, Anna; Bednarczyk-Cwynar, Barbara; Zaprutko, Lucjusz; Gzella, Andrzej

2017-05-01

Synthesis, spectral and X-ray analysis of three compounds, i.e. 3β-acetoxy-12-hydroxyimino-18β-oleanan-28,13β-olide (substrate) and 3β-acetoxy-12-nitrile-12,13-seco-15(14 → 13)-abeoolean-14(27)-en-28,13β-olide and 3β-acetoxy-12-oxo-12a-aza-C-homoolean-13(18)-en-28-oic acid (Beckmann rearrangement reaction products) are described. Structural analysis revealed that the oxime group in the ring C in substrate molecule had an E-configuration. The nitrile product with retained lactone group was a result of major transformations within rings C and D of oleanane skeleton. In lactam product free carboxyl group and a double bond in ring D instead of lactone system were formed in Beckmann rearrangement reaction.

Iridium-Catalyzed Dynamic Kinetic Isomerization: Expedient Synthesis of Carbohydrates from Achmatowicz Rearrangement Products.

PubMed

Wang, Hao-Yuan; Yang, Ka; Bennett, Scott R; Guo, Sheng-rong; Tang, Weiping

2015-07-20

A highly stereoselective dynamic kinetic isomerization of Achmatowicz rearrangement products was discovered. This new internal redox isomerization provided ready access to key intermediates for the enantio- and diastereoselective synthesis of a series of naturally occurring sugars. The nature of the de novo synthesis also enables the preparation of both enantiomers. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Pilot-scale study on the acid-catalyzed steam explosion of rice straw using a continuous pretreatment system.

PubMed

Chen, Wen-Hua; Tsai, Chia-Chin; Lin, Chih-Feng; Tsai, Pei-Yuan; Hwang, Wen-Song

2013-01-01

A continuous acid-catalyzed steam explosion pretreatment process and system to produce cellulosic ethanol was developed at the pilot-scale. The effects of the following parameters on the pretreatment efficiency of rice straw feedstocks were investigated: the acid concentration, the reaction temperature, the residence time, the feedstock size, the explosion pressure and the screw speed. The optimal presteaming horizontal reactor conditions for the pretreatment process are as follows: 1.7 rpm and 100-110 °C with an acid concentration of 1.3% (w/w). An acid-catalyzed steam explosion is then performed in the vertical reactor at 185 °C for 2 min. Approximately 73% of the total saccharification yield was obtained after the rice straw was pretreated under optimal conditions and subsequent enzymatic hydrolysis at a combined severity factor of 0.4-0.7. Moreover, good long-term stability and durability of the pretreatment system under continuous operation was observed. Copyright © 2012 Elsevier Ltd. All rights reserved.

Conversion of Arylboronic Acids to Tetrazoles Catalyzed by ONO Pincer-Type Palladium Complex.

PubMed

Vignesh, Arumugam; Bhuvanesh, Nattamai S P; Dharmaraj, Nallasamy

2017-01-20

A convenient synthesis of a library of tetrazoles through a novel and operationally simple protocol effecting the direct conversion of arylboronic acids catalyzed by a new ONO pincer-type Pd(II) complex under mild reaction conditions using the readily available reagents is reported. The palladium complex was reused up to four cycles in an open-flask condition.

Direct Synthesis of 5-Aryl Barbituric Acids by Rhodium(II)-Catalyzed Reactions of Arenes with Diazo Compounds**

PubMed Central

Best, Daniel; Burns, David J; Lam, Hon Wai

2015-01-01

A commercially available rhodium(II) complex catalyzes the direct arylation of 5-diazobarbituric acids with arenes, allowing straightforward access to 5-aryl barbituric acids. Free N—H groups are tolerated on the barbituric acid, with no complications arising from N—H insertion processes. This method was applied to the concise synthesis of a potent matrix metalloproteinase (MMP) inhibitor. PMID:25959544

Indium-Catalyzed Reductive Dithioacetalization of Carboxylic Acids with Dithiols: Scope, Limitations, and Application to Oxidative Desulfurization.

PubMed

Nishino, Kota; Minato, Kohei; Miyazaki, Takahiro; Ogiwara, Yohei; Sakai, Norio

2017-04-07

In this study an InI 3 -TMDS (1,1,3,3-tetramethyldisiloxane) reducing system effectively catalyzed the reductive dithioacetalization of a variety of aromatic and aliphatic carboxylic acids with 1,2-ethanedithiol or 1,3-propanedithiol leading to the one-pot preparation of either 1,3-dithiolane derivatives or a 1,3-dithiane derivative. Also, the intact indium catalyst continuously catalyzed the subsequent oxidative desulfurization of an in situ formed 1,3-dithiolane derivative, which led to the preparation of the corresponding aldehydes.

Sequential Aldol Condensation – Transition Metal-Catalyzed Addition Reactions of Aldehydes, Methyl Ketones and Arylboronic Acids

PubMed Central

Liao, Yuan-Xi; Xing, Chun-Hui; Israel, Matthew; Hu, Qiao-Sheng

2011-01-01

Sequential aldol condensation of aldehydes with methyl ketones followed by transition metal-catalyzed addition reactions of arylboronic acids to form β-substituted ketones is described. By using the 1,1′-spirobiindane-7,7′-diol (SPINOL)-based phosphite, an asymmetric version of this type of sequential reaction, with up to 92% ee, was also realized. Our study provided an efficient method to access β-substituted ketones and might lead to the development of other sequential/tandem reactions with transition metal-catalyzed addition reactions as the key step. PMID:21417359

β-Amino acid catalyzed asymmetric Michael additions: design of organocatalysts with catalytic acid/base dyad inspired by serine proteases.

PubMed

Yang, Hui; Wong, Ming Wah

2011-09-16

A new type of chiral β-amino acid catalyst has been computationally designed, mimicking the enzyme catalysis of serine proteases. Our catalyst approach is based on the bioinspired catalytic acid/base dyad, namely, a carboxyl and imidazole pair. DFT calculations predict that this designed organocatalyst catalyzes Michael additions of aldehydes to nitroalkenes with excellent enantioselectivities and remarkably high anti diastereoselectivities. The unusual stacked geometry of the enamine intermediate, hydrogen bonding network, and the adoption of an exo transition state are the keys to understand the stereoselectivity. © 2011 American Chemical Society

Regioselective, borinic acid-catalyzed monoacylation, sulfonylation and alkylation of diols and carbohydrates: expansion of substrate scope and mechanistic studies.

PubMed

Lee, Doris; Williamson, Caitlin L; Chan, Lina; Taylor, Mark S

2012-05-16

Synthetic and mechanistic aspects of the diarylborinic acid-catalyzed regioselective monofunctionalization of 1,2- and 1,3-diols are presented. Diarylborinic acid catalysis is shown to be an efficient and general method for monotosylation of pyranoside derivatives bearing three secondary hydroxyl groups (7 examples, 88% average yield). In addition, the scope of the selective acylation, sulfonylation, and alkylation is extended to 1,2- and 1,3-diols not derived from carbohydrates (28 examples); the efficiency, generality, and operational simplicity of this method are competitive with those of state-of-the-art protocols including the broadly applied organotin-catalyzed or -mediated reactions. Mechanistic details of the organoboron-catalyzed processes are explored using competition experiments, kinetics, and catalyst structure-activity relationships. These experiments are consistent with a mechanism in which a tetracoordinate borinate complex reacts with the electrophilic species in the turnover-limiting step of the catalytic cycle.

QUANTITATION OF ABERRANT INTERLOCUS T-CELL RECEPTOR REARRANGEMENTS IN MOUSE THYMOCYTES AND THE EFFECT OF THE HERBICIDE 2,4- DICHLOROPHENOXYACETIC ACID

EPA Science Inventory

Quantitation of aberrant interlocus T-cell receptor rearrangements in mouse thymocytes and the effect of the herbicide 2,4- Dichlorophenoxyacetic acid

Small studies in human populations have suggested a correlation between the frequency of errors in antigen receptor gene a...

Kinetics of Maleic Acid and Aluminum Chloride Catalyzed Dehydration and Degradation of Glucose

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Ximing; Hewetson, Barron B.; Mosier, Nathan S.

We report the positive effect of maleic acid, a dicarboxylic acid, on the selectivity of hexose dehydration to 5-hydroxymethyfurfural (HMF) and subsequent hydrolysis to levulinic and formic acids. We also describe the kinetic analysis of a Lewis acid (AlCl3) alone and in combination with HCl or maleic acid to catalyze the isomerization of glucose to fructose, dehydration of fructose to HMF, hydration of HMF to levulinic and formic acids, and degradation of these compounds to humins. The results show that AlCl3 significantly enhances the rate of glucose conversion to HMF and levulinic acid in the presence of both maleic acidmore » and HCl. In addition, the degradation of HMF to humins, rather than levulinic and formic acids, is reduced by 50% in the presence of maleic acid and AlCl3 compared to HCl combined with AlCl3. The results suggest different reaction mechanisms for the dehydration of glucose and rehydration of HMF between maleic acid and HCl.« less

Copper(II)-Catalyzed Conversion of Aryl/Heteroaryl Boronic Acids, Boronates, and Trifluoroborates into the Corresponding Azides: Substrate Scope and Limitations.

PubMed

Grimes, Kimberly D; Gupte, Amol; Aldrich, Courtney C

2010-05-01

We report the copper(II)-catalyzed conversion of organoboron compounds into the corresponding azide derivatives. A systematic series of phenylboronic acid derivatives is evaluated to examine the importance of steric and electronic effects of the substituents on reaction yield as well as functional group compatibility. Heterocyclic substrates are also shown to participate in this mild reaction while compounds incorporating B-C(sp(3)) bonds are unreactive under the reaction conditions. The copper(II)-catalyzed boronic acid-azide coupling reaction is further extended to both boronate esters and potassium organotrifluoroborate salts. The method described herein complements existing procedures for the preparation of aryl azides from the respective amino, triazene, and halide derivatives and we expect that it will greatly facilitate copper- and ruthenium-catalyzed azide-alkyne cycloaddition reactions for the preparation of diversely functionalized 1-aryl- or 1-heteroaryl-1,2,3-triazoles derivatives.

Flavin-mediated dual oxidation controls an enzymatic Favorskii-type rearrangement

PubMed Central

Louie, Gordon; Noel, Joseph P.; Baran, Phil S.; Palfey, Bruce; Moore, Bradley S.

2013-01-01

Flavoproteins catalyze a diversity of fundamental redox reactions and are one of the most studied enzyme families1,2. As monooxygenases, they are universally thought to control oxygenation by means of a peroxyflavin species that transfers a single atom of molecular oxygen to an organic substrate1,3,4. Here we report that the bacterial flavoenzyme EncM5,6 catalyzes the peroxyflavin-independent oxygenation-dehydrogenation dual oxidation of a highly reactive poly(β-carbonyl). The crystal structure of EncM with bound substrate mimics coupled with isotope labeling studies reveal previously unknown flavin redox biochemistry. We show that EncM maintains an unanticipated stable flavin oxygenating species, proposed to be a flavin-N5-oxide, to promote substrate oxidation and trigger a rare Favorskii-type rearrangement that is central to the biosynthesis of the antibiotic enterocin. This work provides new insight into the fine-tuning of the flavin cofactor in offsetting the innate reactivity of a polyketide substrate to direct its efficient electrocyclization. PMID:24162851

Regioselective and enantiospecific rhodium-catalyzed allylic alkylation reactions using copper(I) enolates: synthesis of (-)-sugiresinol dimethyl ether.

PubMed

Evans, P Andrew; Leahy, David K

2003-07-30

The transition metal-catalyzed allylic alkylation represents a fundamentally important cross-coupling reaction for the construction of ternary carbon stereogenic centers. We have developed a regioselective and enantiospecific rhodium-catalyzed allylic alkylation of acyclic unsymmetrical allylic alcohol derivatives using copper(I) enolates to prepare beta-substituted ketones. This protocol represents a convenient asymmetric Claisen rearrangement surrogate in which alpha-substituted enolates permit the introduction of an additional stereogenic center. The synthetic utility of this transformation was highlighted in the construction of a trans-1,2-disubstituted cyclohexene and the total synthesis of (-)-sugiresinol dimethyl ether. Finally, we anticipate that copper(I) enolates may prove useful nucleophiles in related metal-catalyzed reactions.

Alkali-catalyzed low temperature wet crosslinking of plant proteins using carboxylic acids.

PubMed

Reddy, Narendra; Li, Ying; Yang, Yiqi

2009-01-01

We report the development of a new method of alkali-catalyzed low temperature wet crosslinking of plant proteins to improve their breaking tenacity without using high temperatures or phosphorus-containing catalysts used in conventional poly(carboxylic acid) crosslinking of cellulose and proteins. Carboxylic acids are preferred over aldehyde-containing crosslinkers for crosslinking proteins and cellulose because of their low toxicity and cost and ability to improve the desired properties of the materials. However, current knowledge in carboxylic acid crosslinking of proteins and cellulose requires the use of carboxylic acids with at least three carboxylic groups, toxic phosphorous-containing catalysts and curing at high temperatures (150-185 degrees C). The use of high temperatures and low pH in conventional carboxylic acid crosslinking has been reported to cause substantial strength loss and/or undesired changes in the properties of the crosslinked materials. In this research, gliadin, soy protein, and zein fibers have been crosslinked with malic acid, citric acid, and butanetetracarboxylic acid to improve the tenacity of the fibers without using high temperatures and phosphorus-containing catalysts. The new method of wet crosslinking using carboxylic acids containing two or more carboxylic groups will be useful to crosslink proteins for various industrial applications.

Selenium-mediated synthesis of biaryls through rearrangement.

PubMed

Shahzad, Sohail A; Vivant, Clotilde; Wirth, Thomas

2010-03-19

A new cyclization of beta-keto ester substituted stilbene derivatives using selenium electrophiles in the presence of Lewis acids is described. Substituted naphthols are obtained through cyclization and subsequent 1,2-rearrangement of aryl groups under very mild reaction conditions.

Ru (III) Catalyzed Oxidation of Aliphatic Ketones by N-Bromosuccinimide in Aqueous Acetic Acid: A Kinetic Study

PubMed Central

Giridhar Reddy, P.; Ramesh, K.; Shylaja, S.; Rajanna, K. C.; Kandlikar, S.

2012-01-01

Kinetics of Ru (III) catalyzed oxidation of aliphatic ketones such as acetone, ethyl methyl ketone, diethyl ketone, iso-butylmethyl ketone by N-bromosuccinimide in the presence of Hg(II) acetate have been studied in aqueous acid medium. The order of [N-bromosuccinimide] was found to be zero both in catalyzed as well as uncatalyzed reactions. However, the order of [ketone] changed from unity to a fractional one in the presence of Ru (III). On the basis of kinetic features, the probable mechanisms are discussed and individual rate parameters evaluated. PMID:22654610

Exploiting the CNC side chain in heterocyclic rearrangements: synthesis of 4(5)-acylamino-imidazoles.

PubMed

Piccionello, Antonio Palumbo; Buscemi, Silvestre; Vivona, Nicolò; Pace, Andrea

2010-08-06

A new variation on the Boulton-Katritzky reaction is reported, namely, involving use of a CNC side chain. A novel Montmorillonite-K10 catalyzed nonreductive transamination of a 3-benzoyl-1,2,4-oxadiazole afforded a 3-(alpha-aminobenzyl)-1,2,4-oxadiazole, which was condensed with benzaldehydes to afford the corresponding imines. In the presence of strong base, these imines underwent Boulton-Katritzky-type rearrangement to afford novel 4(5)-acylaminoimidazoles.

Identification of activities that catalyze the cis-trans isomerization of the double bond of a mono-unsaturated fatty acid in Pseudomonas sp. strain E-3.

PubMed

Okuyama, H; Enari, D; Shibahara, A; Yamamoto, K; Morita, N

1996-06-01

A cell-free extract of Pseudomonas sp. strain E-3 catalyzed the conversion of 9-cis-hexadecenoic acid [16:1(9c)] to 9-trans-hexadecenoic acid [16:1(9t)] in the free acid form and when 16:1(9c) was esterified to phosphatidylethanolamine (PE). The cytosolic fraction catalyzed the isomerizations of free 16:1(9c) by itself and of 16:1(9c) esterified to PE in the presence of the membrane fraction. Tracer experiments using [2,2-2H2]16:1(9c) demonstrated that the isomerization of free 16:1(9c) occurred independently of the isomerization of 16:1(9c) esterified to PE, indicating that this bacterium has two types of activities that catalyze the cis-trans isomerization of the double bond of a mono-unsaturated fatty acid.

The CYP88A cytochrome P450, ent-kaurenoic acid oxidase, catalyzes three steps of the gibberellin biosynthesis pathway

PubMed Central

Helliwell, Chris A.; Chandler, Peter M.; Poole, Andrew; Dennis, Elizabeth S.; Peacock, W. James

2001-01-01

We have shown that ent-kaurenoic acid oxidase, a member of the CYP88A subfamily of cytochrome P450 enzymes, catalyzes the three steps of the gibberellin biosynthetic pathway from ent-kaurenoic acid to GA12. A gibberellin-responsive barley mutant, grd5, accumulates ent-kaurenoic acid in developing grains. Three independent grd5 mutants contain mutations in a gene encoding a member of the CYP88A subfamily of cytochrome P450 enzymes, defined by the maize Dwarf3 protein. Mutation of the Dwarf3 gene gives rise to a gibberellin-responsive dwarf phenotype, but the lesion in the gibberellin biosynthesis pathway has not been identified. Arabidopsis thaliana has two CYP88A genes, both of which are expressed. Yeast strains expressing cDNAs encoding each of the two Arabidopsis and the barley CYP88A enzymes catalyze the three steps of the GA biosynthesis pathway from ent-kaurenoic acid to GA12. Sequence comparison suggests that the maize Dwarf3 locus also encodes ent-kaurenoic acid oxidase. PMID:11172076

Electrochemical synthesis of formic acid from CO2 catalyzed by Shewanella oneidensis MR-1 whole-cell biocatalyst.

PubMed

Le, Quang Anh Tuan; Kim, Hee Gon; Kim, Yong Hwan

2018-09-01

The electro-biocatalytic conversion of CO 2 into formic acid using whole-cell and isolated biocatalysts is useful as an alternative route for CO 2 sequestration. In this study, Shewanella oneidensis MR-1 (S. oneidensis MR-1), a facultative aerobic bacterium that has been extensively studied for its utility as biofuel cells as well as for the detoxification of heavy metal oxides (i.e., MnO 2 , uranium), has been applied for the first time as a whole-cell biocatalyst for formic acid synthesis from gaseous CO 2 and electrons supplied from an electrode. S. oneidensis MR-1, when aerobically grown in Luria-Bertani (LB) medium, exhibited its ability as a whole-cell biocatalyst for the conversion of CO 2 into formic acid with moderate productivity of 0.59 mM h -1 for 24 h. In addition, an optimization of growth conditions of S. oneidensis MR-1 resulted in a remarkable increase in productivity. The CO 2 reduction reaction catalyzed by S. oneidensis MR-1, when anaerobically grown in newly optimized LB medium supplemented with fumarate and nitrate, exhibited 3.2-fold higher productivity (1.9 mM h -1 for 72 h) compared to that grown aerobically in only LB medium. Furthermore, the average conversion rate of formic acid synthesis catalyzed by S. oneidensis MR-1 when grown in the optimal medium over a period of 72 h was 3.8 mM h -1  g -1 wet-cell, which is 9.6-fold higher than that catalyzed by Methylobacterium extorquens AM1 whole-cells in our previous study. Copyright © 2018 Elsevier Inc. All rights reserved.

Stereochemical analysis of the elimination reaction catalyzed by D-amino-acid oxidase.

PubMed

Cheung, Y F; Walsh, C

1976-06-01

The stereochemistry of the intramolecular proton transfer catalyzed by the flavoenzyme, D-amino-acid oxidase, during the elimination reaction of beta-chloro-alpha-amino acid substrates (Walsh et al. (1973), J. Biol. Chem. 248, 1964) has been established. Both D-erythro- and D-threo-2-amino-3-chloro(2-3H) butyrate have been shown to yield (3R)-2-keto (3-3H)-2- butyrate predominantly. Tritium kinetic isotope effects on the rate of the reaction (4.7 for the D-erythro, and 3.8 for the D-threo compound) and percentages of intramolecular triton transfer (7.2% for the D-erythro- and 2.6% for the D-threo compound) have been measured. Their implications on the mechanism of this unusual elimination reaction are discussed.

Acid-catalyzed ring-opening reactions of a cyclopropanated 3-aza-2-oxabicyclo[2.2.1]hept-5-ene with alcohols.

PubMed

Tait, Katrina; Horvath, Alysia; Blanchard, Nicolas; Tam, William

2017-01-01

The acid-catalyzed ring-opening reactions of a cyclopropanated 3-aza-2-oxabicylic alkene using alcohol nucleophiles were investigated. Although this acid-catalyzed ring-opening reaction did not cleave the cyclopropane unit as planned, this represent the first examples of ring-openings of cyclopropanated 3-aza-2-oxabicyclo[2.2.1]alkenes that lead to the cleavage of the C-O bond instead of the N-O bond. Different acid catalysts were tested and it was found that pyridinium toluenesulfonate in methanol gave the best yields in the ring-opening reactions. The scope of the reaction was successfully expanded to include primary, secondary, and tertiary alcohol nucleophiles. Through X-ray crystallography, the stereochemistry of the product was determined which confirmed an S N 2-like mechanism to form the ring-opened product.

Behaviors of glucose decomposition during acid-catalyzed hydrothermal hydrolysis of pretreated Gelidium amansii.

PubMed

Jeong, Tae Su; Choi, Chang Ho; Lee, Ji Ye; Oh, Kyeong Keun

2012-07-01

Acid-catalyzed hydrothermal hydrolysis is one path to cellulosic glucose and subsequently to its dehydration end products such as hydroxymethyl furfural (HMF), formic acid and levulinic acid. The effect of sugar decomposition not only lowers the yield of fermentable sugars but also forms decomposition products that inhibit subsequent fermentation. The present experiments were conducted with four different acid catalysts (H(2)SO(4), HNO(3), HCl, and H(3)PO(4)) at various acid normalities (0.5-2.1N) in batch reactors at 180-210 °C. From the results, H(2)SO(4) was the most suitable catalyst for glucose production, but glucose decomposition occurred during the hydrolysis. The glucose production was maximized at 160.7 °C, 2.0% (w/v) H(2)SO(4), and 40 min, but resulted in a low glucan yield of 33.05% due to the decomposition reactions, which generated formic acid and levulinic acid. The highest concentration of levulinic acid, 7.82 g/L, was obtained at 181.2 °C, 2.0% (w/v) H(2)SO(4), and 40 min. Copyright © 2012 Elsevier Ltd. All rights reserved.

Silver-catalyzed double-decarboxylative cross-coupling of α-keto acids with cinnamic acids in water: a strategy for the preparation of chalcones.

PubMed

Zhang, Ning; Yang, Daoshan; Wei, Wei; Yuan, Li; Nie, Fafa; Tian, Laijin; Wang, Hua

2015-03-20

A silver-catalyzed double-decarboxylative protocol has been proposed for the construction of chalcone derivatives via cascade coupling of substituted α-keto acids with cinnamic acids under the mild aqueous conditions. The developed method for constructing C-C bonds via double-decarboxylative reactions is efficient, practical, and environmentally benign by using the readily available starting materials. It should provide a promising synthesis candidate for the formation of diverse and useful chalcone derivatives in the fields of synthetic and pharmaceutical chemistry.

Mild partial deoxygenation of esters catalyzed by an oxazolinylborate-coordinated rhodium silylene

DOE PAGES

Xu, Songchen; Boschen, Jeffery S.; Biswas, Abhranil; ...

2015-08-17

An electrophilic, coordinatively unsaturated rhodium complex supported by borate-linked oxazoline, oxazoline-coordinated silylene, and N-heterocyclic carbene donors [{κ³-N,Si,C-PhB(Ox Me²)(Ox Me²SiHPh)Im Mes}Rh(H)CO][HB(C₆F₅)₃] (2, Ox Me² = 4,4-dimethyl-2-oxazoline; Im Mes = 1-mesitylimidazole) is synthesized from the neutral rhodium silyl {PhB(Ox Me²)₂Im Mes}RhH(SiH 2Ph)CO (1) and B(C 6F 5) 3. The unusual oxazoline-coordinated silylene structure in 2 is proposed to form by rearrangement of an unobserved isomeric cationic rhodium silylene species [{PhB(Ox Me²)₂Im Mes}RhH(SiHPh)CO][HB(C₆F₅)₃] generated by H abstraction. Complex 2 catalyzes reductions of organic carbonyl compounds with silanes to give hydrosilylation products or deoxygenation products. The pathway to these reactions is primarily influenced bymore » the degree of substitution of the organosilane. Reactions with primary silanes give deoxygenation of esters to ethers, amides to amines, and ketones and aldehydes to hydrocarbons, whereas tertiary silanes react to give 1,2-hydrosilylation of the carbonyl functionality. In contrast, the strong Lewis acid B(C₆F₅)₃ catalyzes the complete deoxygenation of carbonyl compounds to hydrocarbons with PhSiH₃ as the reducing agent.« less

Mild partial deoxygenation of esters catalyzed by an oxazolinylborate-coordinated rhodium silylene

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xu, Songchen; Boschen, Jeffery S.; Biswas, Abhranil

An electrophilic, coordinatively unsaturated rhodium complex supported by borate-linked oxazoline, oxazoline-coordinated silylene, and N-heterocyclic carbene donors [{κ³-N,Si,C-PhB(Ox Me²)(Ox Me²SiHPh)Im Mes}Rh(H)CO][HB(C₆F₅)₃] (2, Ox Me² = 4,4-dimethyl-2-oxazoline; Im Mes = 1-mesitylimidazole) is synthesized from the neutral rhodium silyl {PhB(Ox Me²)₂Im Mes}RhH(SiH 2Ph)CO (1) and B(C 6F 5) 3. The unusual oxazoline-coordinated silylene structure in 2 is proposed to form by rearrangement of an unobserved isomeric cationic rhodium silylene species [{PhB(Ox Me²)₂Im Mes}RhH(SiHPh)CO][HB(C₆F₅)₃] generated by H abstraction. Complex 2 catalyzes reductions of organic carbonyl compounds with silanes to give hydrosilylation products or deoxygenation products. The pathway to these reactions is primarily influenced bymore » the degree of substitution of the organosilane. Reactions with primary silanes give deoxygenation of esters to ethers, amides to amines, and ketones and aldehydes to hydrocarbons, whereas tertiary silanes react to give 1,2-hydrosilylation of the carbonyl functionality. In contrast, the strong Lewis acid B(C₆F₅)₃ catalyzes the complete deoxygenation of carbonyl compounds to hydrocarbons with PhSiH₃ as the reducing agent.« less

Late-Stage Functionalization of Arylacetic Acids by Photoredox-Catalyzed Decarboxylative Carbon-Heteroatom Bond Formation.

PubMed

Sakakibara, Yota; Ito, Eri; Fukushima, Tomohiro; Murakami, Kei; Itami, Kenichiro

2018-05-02

The rapid transformation of pharmaceuticals and agrochemicals enables access to unexplored chemical space and thus has accelerated the discovery of novel bioactive molecules. Because arylacetic acids are regarded as key structures in bioactive compounds, new transformations of these structures could contribute to drug/agrochemical discovery and chemical biology. This work reports carbon-nitrogen and carbon-oxygen bond formation through the photoredox-catalyzed decarboxylation of arylacetic acids. The reaction shows good functional group compatibility without pre-activation of the nitrogen- or oxygen-based coupling partners. Under similar reaction conditions, carbon-chlorine bond formation was also feasible. This efficient derivatization of arylacetic acids makes it possible to synthesize pharmaceutical analogues and bioconjugates of pharmaceuticals and natural products. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Kinetics of acid base catalyzed transesterification of Jatropha curcas oil.

PubMed

Jain, Siddharth; Sharma, M P

2010-10-01

Out of various non-edible oil resources, Jatropha curcas oil (JCO) is considered as future feedstock for biodiesel production in India. Limited work is reported on the kinetics of transesterification of high free fatty acids containing oil. The present study reports the results of kinetic study of two-step acid base catalyzed transesterification process carried out at an optimum temperature of 65 °C and 50 °C for esterification and transesterification respectively under the optimum methanol to oil ratio of 3:7 (v/v), catalyst concentration 1% (w/w) for H₂SO₄ and NaOH. The yield of methyl ester (ME) has been used to study the effect of different parameters. The results indicate that both esterification and transesterification reaction are of first order with reaction rate constant of 0.0031 min⁻¹ and 0.008 min⁻¹ respectively. The maximum yield of 21.2% of ME during esterification and 90.1% from transesterification of pretreated JCO has been obtained. Copyright © 2010 Elsevier Ltd. All rights reserved.

Synthesis of 2-monoacylglycerols and structured triacylglycerols rich in polyunsaturated fatty acids by enzyme catalyzed reactions.

PubMed

Rodríguez, Alicia; Esteban, Luis; Martín, Lorena; Jiménez, María José; Hita, Estrella; Castillo, Beatriz; González, Pedro A; Robles, Alfonso

2012-08-10

This paper studies the synthesis of structured triacylglycerols (STAGs) by a four-step process: (i) obtaining 2-monoacylglycerols (2-MAGs) by alcoholysis of cod liver oil with several alcohols, catalyzed by lipases Novozym 435, from Candida antartica and DF, from Rhizopus oryzae, (ii) purification of 2-MAGs, (iii) formation of STAGs by esterification of 2-MAGs with caprylic acid catalyzed by lipase DF, from R. oryzae, and (iv) purification of these STAGs. For the alcoholysis of cod liver oil, absolute ethanol, ethanol 96% (v/v) and 1-butanol were compared; the conditions with ethanol 96% were then optimized and 2-MAG yields of around 54-57% were attained using Novozym 435. In these 2-MAGs, DHA accounted for 24-31% of total fatty acids. In the operational conditions this lipase maintained a stable level of activity over at least 11 uses. These results were compared with those obtained with lipase DF, which deactivated after only three uses. The alcoholysis of cod liver oil and ethanol 96% catalyzed by Novozym 435 was scaled up by multiplying the reactant amounts 100-fold and maintaining the intensity of treatment constant (IOT=3g lipase h/g oil). In these conditions, the 2-MAG yield attained was about 67%; these 2-MAGs contained 36.6% DHA. The synthesized 2-MAGs were separated and purified from the alcoholysis reaction products by solvent extraction using solvents of low toxicity (ethanol and hexane); 2-MAG recovery yield and purity of the target product were approximately 96.4% and 83.9%, respectively. These 2-MAGs were transformed to STAGs using the optimal conditions obtained in a previous work. After synthesis and purification, 93% pure STAGs were obtained, containing 38% DHA at sn-2 position and 60% caprylic acid (CA) at sn-1,3 positions (of total fatty acids at these positions), i.e. the major TAG is the STAG with the structure CA-DHA-CA. Copyright © 2012 Elsevier Inc. All rights reserved.

Complex Biotransformations Catalyzed by Radical S-Adenosylmethionine Enzymes*

PubMed Central

Zhang, Qi; Liu, Wen

2011-01-01

The radical S-adenosylmethionine (AdoMet) superfamily currently comprises thousands of proteins that participate in numerous biochemical processes across all kingdoms of life. These proteins share a common mechanism to generate a powerful 5′-deoxyadenosyl radical, which initiates a highly diverse array of biotransformations. Recent studies are beginning to reveal the role of radical AdoMet proteins in the catalysis of highly complex and chemically unusual transformations, e.g. the ThiC-catalyzed complex rearrangement reaction. The unique features and intriguing chemistries of these proteins thus demonstrate the remarkable versatility and sophistication of radical enzymology. PMID:21771780

Formation of Ketenimines via the Palladium-Catalyzed Decarboxylative π-Allylic Rearrangement of N-Alloc Ynamides.

PubMed

Alexander, Juliana R; Cook, Matthew J

2017-11-03

A new approach for the formation of ketenimines via a decarboxylative allylic rearrangement pathway that does not require strong stabilizing or protecting groups has been developed. The products can be readily hydrolyzed into their corresponding secondary amides or reacted with sulfur ylides to perform an additional [2,3]-Wittig process. Mechanistic studies suggest an outer-sphere process in which reductive alkylation is rate-limiting.

Brønsted acid-catalyzed decarboxylative redox amination: formation of N-alkylindoles from azomethine ylides by isomerization.

PubMed

Mao, Hui; Wang, Sichang; Yu, Peng; Lv, Huiqing; Xu, Runsheng; Pan, Yuanjiang

2011-02-18

A Brønsted acid-catalyzed decarboxylative redox amination involving aldehydes with 2-carboxyindoline for the synthesis of N-alkylindoles is described. The decarboxylative condensations of aldehydes with 2-carboxyindoline produce azomethine ylides in situ, which then transform into N-alkylindoles by isomerization. © 2011 American Chemical Society

Immunoglobulin λ Gene Rearrangement Can Precede κ Gene Rearrangement

DOE PAGES

Berg, Jörg; Mcdowell, Mindy; Jäck, Hans-Martin; ...

1990-01-01

Imore » mmunoglobulin genes are generated during differentiation of B lymphocytes by joining gene segments. A mouse pre-B cell contains a functional immunoglobulin heavy-chain gene, but no light-chain gene. Although there is only one heavy-chain locus, there are two lightchain loci: κ and λ .t has been reported that κ loci in the germ-line configuration are never (in man) or very rarely (in the mouse) present in cells with functionally rearranged λ -chain genes. Two explanations have been proposed to explain this: (a) the ordered rearrangement theory, which postulates that light-chain gene rearrangement in the pre-B cell is first attempted at the κ locus, and that only upon failure to produce a functional κ chain is there an attempt to rearrange the λ locus; and (b) the stochastic theory, which postulates that rearrangement at the λ locus proceeds at a rate that is intrinsically much slower than that at the κ locus. We show here that λ -chain genes are generated whether or not the κ locus has lost its germ-line arrangement, a result that is compatible only with the stochastic theory.« less

Copper(II)-catalyzed hydroxylation of aryl halides using glycolic acid as a ligand.

PubMed

Xiao, Yan; Xu, Yongnan; Cheon, Hwan-Sung; Chae, Junghyun

2013-06-07

Copper(II)-catalyzed hydroxylation of aryl halides has been developed to afford functionalized phenols. The protocol utilizes the reagent combination of Cu(OH)2, glycolic acid, and NaOH in aqueous DMSO, all of which are cheap, readily available, and easily removable after the reaction. A broad range of aryl iodides and activated aryl bromides were transformed into the corresponding phenols in excellent yields. Moreover, it has been shown that C-O(alkyl)-coupled product, instead of phenol, can be predominantly formed under similar reaction conditions.

Modeling the reactions catalyzed by coenzyme B12-dependent enzymes.

PubMed

Sandala, Gregory M; Smith, David M; Radom, Leo

2010-05-18

Enzymes accelerate chemical reactions with an exceptional selectivity that makes life itself possible. Understanding the factors responsible for this efficient catalysis is of utmost importance in our quest to harness the tremendous power of enzymes. Computational chemistry has emerged as an important adjunct to experimental chemistry and biochemistry in this regard, because it provides detailed insights into the relationship between structure and function in a systematic and straightforward manner. In this Account, we highlight our recent high-level theoretical investigations toward this end in studying the radical-based reactions catalyzed by enzymes dependent on coenzyme B(12) (or adenosylcobalamin, AdoCbl). In addition to their fundamental position in biology, the AdoCbl-dependent enzymes represent a valuable framework within which to understand Nature's method of efficiently handling high-energy species to execute very specific reactions. The AdoCbl-mediated reactions are characterized by the interchange of a hydrogen atom and a functional group on adjacent carbon atoms. Our calculations are consistent with the conclusion that the main role of AdoCbl is to provide a source of radicals, thus moving the 1,2-rearrangements onto the radical potential energy surface. Our studies also show that the radical rearrangement step is facilitated by partial proton transfer involving the substrate. Specifically, we observe that the energy requirements for radical rearrangement are reduced dramatically with appropriate partial protonation or partial deprotonation or sometimes (synergistically) both. Such interactions are particularly relevant to enzyme catalysis, because it is likely that the local amino acid environment in the active site of an enzyme can function in this capacity through hydrogen bonding. Finally, our calculations indicate that the intervention of a very stable radical along the reaction pathway may inactivate the enzyme, demonstrating that sustained

Construction of divergent fused heterocycles via an acid-promoted intramolecular ipso-Friedel-Crafts alkylation of phenol derivatives.

PubMed

Yokosaka, Takuya; Shiga, Naoki; Nemoto, Tetsuhiro; Hamada, Yasumasa

2014-05-02

Two different cascade cyclization processes were developed using aryl group-substituted propargyl alcohol derivatives with a p-hydroxybenzylamine unit as common substrates. Using TFA as an acid promoter, an intramolecular ipso-Friedel-Crafts alkylation of phenol derivatives, formation of an iminium cation via a rearomatization-promoted C-C bond cleavage, an aza-Prins reaction, and a 6-membered ring formation proceeded sequentially, producing a variety of fused-tricyclic dihydroquinoline derivatives in 45-99% yield. In addition, a one-pot sequential silver acetate-catalyzed hydroamination/etherification-acid-promoted skeletal rearrangement was examined using the same series of substrates, affording fused-tricyclic indole/benzofuran derivatives in 66-89% yield.

Direct Synthesis of 5-Aryl Barbituric Acids by Rhodium(II)-Catalyzed Reactions of Arenes with Diazo Compounds.

PubMed

Best, Daniel; Burns, David J; Lam, Hon Wai

2015-06-15

A commercially available rhodium(II) complex catalyzes the direct arylation of 5-diazobarbituric acids with arenes, allowing straightforward access to 5-aryl barbituric acids. Free N-H groups are tolerated on the barbituric acid, with no complications arising from N-H insertion processes. This method was applied to the concise synthesis of a potent matrix metalloproteinase (MMP) inhibitor. © 2015 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Synthesis of 24-phenyl-24-oxo steroids derived from bile acids by palladium-catalyzed cross coupling with phenylboronic acid. NMR characterization and X-ray structures.

PubMed

Mayorquín-Torres, Martha C; Romero-Ávila, Margarita; Flores-Álamo, Marcos; Iglesias-Arteaga, Martin A

2013-11-01

Palladium-catalyzed cross coupling of phenyboronic acid with acetylated bile acids in which the carboxyl functions have been activated by formation of a mixed anhydride with pivalic anhydride afforded moderate to good yield of 24-phenyl-24-oxo-steroids. Unambiguous assignments of the NMR signals were made with the aid of combined 1D and 2D NMR techniques. X-ray diffraction studies confirmed the obtained structures. Copyright © 2013 Elsevier Inc. All rights reserved.

Rearranged diterpenoids from the biotransformation of ent-trachyloban-18-oic acid by Rhizopus arrhizus.

PubMed

Leverrier, Aurélie; Martin, Marie-Thérèse; Servy, Claudine; Ouazzani, Jamal; Retailleau, Pascal; Awang, Khalijah; Mukhtar, Mat Ropi; Guéritte, Françoise; Litaudon, Marc

2010-06-25

In our search for inhibitors of the antiapoptotic protein Bcl-xL, investigation of Xylopia caudata afforded a new diterpenoid, ent-trachyloban-4beta-ol (2), and five known ent-trachylobane or ent-atisane compounds. Only ent-trachyloban-18-oic acid (1) exhibited weak binding activity to Bcl-xL. These compounds exhibited cytotoxicity against KB and HCT-116 cell lines with IC(50) values between 10 and 30 microM. Bioconversion of compound 1 by Rhizopus arrhizus afforded new hydroxylated metabolites (3-7) of the ent-trachylobane and ent-kaurene type and compound 8, with a rearranged pentacyclic carbon framework that was named rhizopene. Compounds 3-8 were noncytotoxic to the two cancer cell lines, and compounds 3 and 5 exhibited only weak binding affinity for Bcl-xL.

General synthesis of C-glycosyl amino acids via proline-catalyzed direct electrophilic alpha-amination of C-glycosylalkyl aldehydes.

PubMed

Nuzzi, Andrea; Massi, Alessandro; Dondoni, Alessandro

2008-10-16

Non-natural axially and equatorially linked C-glycosyl alpha-amino acids (glycines, alanines, and CH2-serine isosteres) with either S or R alpha-configuration were prepared by D- and L-proline-catalyzed (de >95%) alpha-amination of C-glycosylalkyl aldehydes using dibenzyl azodicarboxylate as the electrophilic reagent.

Imidazole catalyzes chlorination by unreactive primary chloramines

PubMed Central

Roemeling, Margo D.; Williams, Jared; Beckman, Joseph S.; Hurst, James K.

2015-01-01

Hypochlorous acid and simple chloramines (RNHCl) are stable biologically-derived chlorinating agents. In general, the chlorination potential of HOCl is much greater than that of RNHCl, allowing it to oxidize or chlorinate a much wider variety of reaction partners. However, in this study we demonstrate by kinetic analysis that the reactivity of RNHCl can be dramatically promoted by imidazole and histidyl model compounds via intermediary formation of the corresponding imidazole chloramines. Two biologically relevant reactions were investigated—loss of imidazole-catalyzed chlorinating capacity and phenolic ring chlorination using fluorescein and the tyrosine analog, 4-hydroxyphenylacetic acid (HPA). HOCl reacted stoichiometrically with imidazole, N-acetylhistidine (NAH), or imidazoleacetic acid to generate the corresponding imidazole chloramines which subsequently decomposed. Chloramine (NH2Cl) also underwent a markedly accelerated loss in chlorinating capacity when NAH was present, although in this case NAHCl did not accumulate, indicating that the catalytic intermediate must be highly reactive. Mixing HOCl with 1-methylimidazole (MeIm) led to very rapid loss in chlorinating capacity via formation of a highly reactive chlorinium ion (MeImCl+) intermediate; this behavior suggests that the reactive forms of the analogous imidazole chloramines are their conjugate acids, e.g., the imidazolechlorinium ion (HImCl+). HOCl-generated imidazole chloramine (ImCl) reacted rapidly with fluorescein in a specific acid-catalyzed second order reaction to give 3′-monochloro and 3′,5′-dichloro products. Equilibrium constants for the transchlorination reactions: HOCl + HIm = H2O + ImCl and NH2Cl + HIm = NH3 + ImCl were estimated from the dependence of the rate constants upon [HIm]/[HOCl] and literature data. Acid catalysis again suggests that the actual chlorinating agent is HImCl+; consistent with this interpretation, MeIm markedly catalyzed fluorescein chlorination by HOCl

Asymmetric synthesis of 5-arylcyclohexenones by rhodium(I)-catalyzed conjugate arylation of racemic 5-(trimethylsilyl)cyclohexenone with arylboronic acids.

PubMed

Chen, Qian; Kuriyama, Masami; Soeta, Takahiro; Hao, Xinyu; Yamada, Ken-ichi; Tomioka, Kiyoshi

2005-09-29

[reaction: see text] A catalytic asymmetric conjugate arylation of racemic 5-(trimethylsilyl)cyclohex-2-enone with arylboronic acids was catalyzed by 3 mol % chiral amidophosphane- or BINAP-Rh(I) in dioxane-water (10:1) to afford trans- and cis-3-aryl-5-(trimethylsilyl)cyclohexanones in high enantioselectivity. Dehydrosilylation of the product mixture with cupric chloride in DMF gave 5-arylcyclohex-2-enones with up to 93% ee in good yield. Enantiofacial selectivity with chiral phosphane-Rh(I) exceeds the trans-diastereoselectivity that is maintained in the achiral or racemic phosphane-Rh(I)-catalyzed conjugate arylation of 5-(trimethylsilyl)cyclohexenone.

Kinetics and mechanism of S-nitrosothiol acid-catalyzed hydrolysis: sulfur activation promotes facile NO+ release.

PubMed

Moran, Ernesto E; Timerghazin, Qadir K; Kwong, Elizabeth; English, Ann M

2011-03-31

The denitrosation of three primary S-nitrosothiols (RSNO; S-nitrosocysteine, S-nitroso-N-acetylcysteine, and S-nitrosoglutathione) and two tertiary RSNOs (S-nitrosopenicillamine and S-nitroso-N-acetylpenicillamine) was investigated in 3.75 M H(2)SO(4) to probe the mechanism of acid-catalyzed RSNO hydrolysis and its dependence on RSNO structure. This reversible reaction was forced to proceed in the denitrosation direction by trapping the nitrosating agent with HN(3). The primary RSNOs exhibited hydrolysis k(obs) values of ∼2 × 10(-4) s(-1), and the tertiary RSNO k(obs) values were an order of magnitude higher. Product analysis by HPLC revealed that the parent thiols (RSHs) were formed in 90-100% yield on 79-99% RSNO denitrosation. Possible hydrolysis mechanisms were studied computationally at the CBS-QB3 level using S-nitrosomethanethiol (MeSNO) as a model RSNO. Consideration of RSNOs as a combination of conventional R-S-N═O, zwitterionic R-S(+)═N-O(-), and RS(-)/NO(+) ion-pair resonance structures was key in understanding the mechanistic details of acid-catalyzed hydrolysis. Protonation of the S-nitroso oxygen or nitrogen activates the sulfur and nucleophilic attack by H(2)O at this atom leads to the formation of the sulfoxide-protonated N-hydroxysulfinamide, MeS(+)(OH)NHOH, with barriers of 19 and 29 kcal/mol, respectively. Proton loss and reprotonation at the nitrogen lead to secondary hydrolysis that produces the sulfinic acid MeS(═O)OH and NH(2)OH. Notably, no low-energy RSNO hydrolysis pathway for HNO release was found in the computational analysis. Protonation of the S-nitroso sulfur gives rise to NO(+) release with a low activation barrier (ΔH(double dagger)(calc) ≈ 6 kcal/mol) and the formation of MeSH in agreement with experiment. The experimental k(obs) can be expressed as K(a)k(1), where K(a) is the acid dissociation constant for protonation of the S-nitroso sulfur and k(1) the pseudo-first-order hydrolysis rate constant. Given the low �

Glutamic acid is an active site residue of angiotensin I-converting enzyme. Use of the Lossen rearrangement for identification of dicarboxylic acid residues.

PubMed

Harris, R B; Wilson, I B

1983-01-25

A set of chemical reactions was used to show that one glutamic acid residue at the active site of bovine lung angiotensin I-converting enzyme is esterified with the alkylating agent p-[N,N-bis(chloroethyl)amino] phenylbutyryl-L-Pro (chlorambucyl-L-Pro), an affinity label for this enzyme (Harris, R. B., and Wilson, I. B. (1982) J. Biol. Chem. 257, 811-815). The same procedure was used to confirm that a glutamic acid residue of carboxypeptidase A alpha is esterified by reaction with bromoacetyl-N-methyl-L-phenylalanine (Haas, G. M., and Neurath, H. (1971) Biochemistry 10, 3535-3546). In the procedure described in this paper, the esterified residue at the active site is converted to the hydroxamic acid by reaction with hydroxylamine and the hydroxamic acid is subject to the Lossen rearrangement. If a glutamic acid residue was esterified, 1 eq of 2,4-diaminobutyric acid will be formed. Aspartyl esters will give 2,3-diaminopropionic acid. The diamino acids can be quantitatively measured using the short column of an amino acid analyzer if the amount of lysine and histidine is largely decreased by modification with suitable side chain protecting groups. With carboxypeptidase A, the reactions were done on the whole undigested enzyme. With the converting enzyme, we first cleaved the esterified enzyme with cyanogen bromide. Twenty-nine cleavage peptides were separated on high performance liquid chromatography and one of these contained all of the bound radioactive inhibitor. This active site peptide was then subjected to the derivatization and Lossen procedures, and 1 eq of 2,4-diaminobutyric acid was obtained.

An intramolecular [2 + 2] cycloaddition of ketenimines via palladium-catalyzed rearrangements of N-allyl-ynamides.

PubMed

DeKorver, Kyle A; Hsung, Richard P; Song, Wang-Ze; Wang, Xiao-Na; Walton, Mary C

2012-06-15

A cascade of Pd-catalyzed N-to-C allyl transfer-intramolecular ketenimine-[2 + 2] cycloadditions of N-allyl ynamides is described. This tandem sequence is highly stereoselective and the [2 + 2] cycloaddition could be rendered in a crossed or fused manner depending on alkene substitutions, leading to bridged and fused bicycloimines.

Fractionation of lignocellulosic biopolymers from sugarcane bagasse using formic acid-catalyzed organosolv process.

PubMed

Suriyachai, Nopparat; Champreda, Verawat; Kraikul, Natthakorn; Techanan, Wikanda; Laosiripojana, Navadol

2018-05-01

A one-step formic acid-catalyzed organosolv process using a low-boiling point acid-solvent system was studied for fractionation of sugarcane bagasse. Compared to H 2 SO 4 , the use of formic acid as a promoter resulted in higher efficiency and selectivity on removals of hemicellulose and lignin with increased enzymatic digestibility of the cellulose-enriched solid fraction. The optimal condition from central composite design analysis was determined as 40 min residence time at 159 °C using water/ethanol/ethyl acetate/formic acid in the respective ratios of 43:20:16:21%v/v. Under this condition, a 94.6% recovery of cellulose was obtained in the solid with 80.2% cellulose content while 91.4 and 80.4% of hemicellulose and lignin were removed to the aqueous-alcohol-acid and ethyl acetate phases, respectively. Enzymatic hydrolysis of the solid yielded 84.5% glucose recovery compared to available glucan in the raw material. Physicochemical analysis revealed intact cellulose fibers with decreased crystallinity while the hemicellulose was partially recovered as mono- and oligomeric sugars. High-purity organosolv lignin with < 1% sugar cross-contamination was obtained with no major structural modification according to Fourier-transform infrared spectroscopy. The work represents an alternative process for efficient fractionation of lignocellulosic biomass in biorefineries.

Asymmetric Synthesis of Hydrocarbazoles Catalyzed by an Octahedral Chiral-at-Rhodium Lewis Acid.

PubMed

Huang, Yong; Song, Liangliang; Gong, Lei; Meggers, Eric

2015-12-01

A bis-cyclometalated chiral-at-metal rhodium complex catalyzes the Diels-Alder reaction between N-Boc-protected 3-vinylindoles (Boc = tert-butyloxycarbonyl) and β-carboxylic ester-substituted α,β-unsaturated 2-acyl imidazoles with good-to-excellent regioselectivity (up to 99:1) and excellent diastereoselectivity (>50:1 d.r.) as well as enantioselectivity (92-99% ee) under optimized conditions. The rhodium catalyst serves as a chiral Lewis acid to activate the 2-acyl imidazole dienophile by two-point binding and overrules the preferred regioselectivity of the uncatalyzed reaction. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

An Intramolecular [2 + 2] Cycloaddition of Ketenimines via Palladium-Catalyzed Rearrangements of N-Allyl-Ynamides

PubMed Central

DeKorver, Kyle A.; Song, Wang-Ze; Wang, Xiao-Na; Walton, Mary C.

2012-01-01

A cascade of Pd-catalyzed N-to-C allyl transfer–intramolecular ketenimine–[2 + 2] cycloadditions of N-allyl ynamides is described. This tandem sequence is highly stereoselective and the [2 + 2] cycloaddition could be rendered in a crossed or fused manner depending on alkene substitutions, leading to bridged and fused bicycloimines. PMID:22667819

Isotope Effects and Mechanism of the Asymmetric BOROX Brønsted Acid Catalyzed Aziridination Reaction

PubMed Central

Vetticatt, Mathew J.; Desai, Aman A.; Wulff, William D.

2013-01-01

The mechanism of the chiral VANOL-BOROX Brønsted acid catalyzed aziridination reaction of imines and ethyldiazoacetate has been studied using a combination of experimental kinetic isotope effects and theoretical calculations. A stepwise mechanism where reversible formation of a diazonium ion intermediate precedes rate-limiting ring-closure to form the cis-aziridine is implicated. A revised model for the origin of enantio- and diastereoselectivity is proposed based on relative energies of the ring closing transition structures. PMID:23687986

Formation of Amino Acid Thioesters for Prebiotic Peptide Synthesis: Catalysis By Amino Acid Products

NASA Technical Reports Server (NTRS)

Weber, Arthur L.; DeVincenzi, Donald L. (Technical Monitor)

1999-01-01

The origin of life can be described as a series of events in which a prebiotic chemical process came increasingly under the control of its catalytic products. In our search for this prebiotic process that yielded catalytic takeover products (such as polypeptides), we have been investigating a reaction system that generates peptide-forming amino acid thioesters from formaldehyde, glycolaldehyde, and ammonia in the presence of thiols. As shown below, this model process begins by aldol condensation of formaldehyde and glycolaldehyde to give trioses and releases. These sugars then undergo beta-dehydration yielding their respective alpha-ketoaldehydes. Addition of ammonia to the alpha-ketoaldehydes yields imines which can either: (a) rearrange in the presence of thesis to give amino acid thioesters or (be react with another molecule of aldehyde to give imidazoles. This 'one-pot' reaction system operates under mild aqueous conditions, and like modem amino acid biosynthesis, uses sugar intermediates which are converted to products by energy-yielding redox reactions. Recently, we discovered that amino acids, such as the alanine reaction product, catalyze the first and second steps of the process. In the presence of ammonia the process also generates other synthetically useful products, like the important biochemical -- pyruvic acid.

Semicontinuous measurements of organic carbon and acidity during the Pittsburgh air quality study: implications for acid-catalyzed organic aerosol formation

DOE Office of Scientific and Technical Information (OSTI.GOV)

S. Takahama; C.I. Davidson; S.N. Pandis

2006-04-01

Laboratory evidence suggests that inorganic acid seed particles may increase secondary organic aerosol yields secondary organic aerosol (SOA) through heterogeneous chemistry. Additional laboratory studies, however, report that organic acidity generated in the same photochemical process by which SOA is formed may be sufficient to catalyze these heterogeneous reactions. Understanding the interaction between inorganic acidity and SOA mass is important when evaluating emission controls to meet PM2.5 regulations. Semicontinuous measurements of organic carbon (OC), elemental carbon (EC), and inorganic species from the Pittsburgh Air Quality Study were examined to determine if coupling in the variations of inorganic acidity and OC couldmore » be detected. Significant enhancements of SOA production could not be detected due to inorganic acidity in Western Pennsylvania most of the time, but its signal might have been lost in the noise. If a causal relationship between inorganic acidity and OC is assumed, reductions in OC for Western Pennsylvania that might result from drastic reductions in inorganic acidity were estimated to be 2 {+-} 4% by a regression technique, and an upper bound for this geographic area was estimated to be 5 {+-} 8% based on calculations from laboratory measurements. 48 refs., 7 figs., 3 tabs.« less

Computational Study of Formic Acid Dehydrogenation Catalyzed by Al(III)-Bis(imino)pyridine.

PubMed

Lu, Qian-Qian; Yu, Hai-Zhu; Fu, Yao

2016-03-18

The mechanism of formic acid dehydrogenation catalyzed by the bis(imino)pyridine-ligated aluminum hydride complex (PDI(2-))Al(THF)H (PDI=bis(imino)pyridine) was studied by density functional theory calculations. The overall transformation is composed of two stages: catalyst activation and the catalytic cycle. The catalyst activation begins with O-H bond cleavage of HCOOH promoted by aluminum-ligand cooperation, followed by HCOOH-assisted Al-H bond cleavage, and protonation of the imine carbon atom of the bis(imino)pyridine ligand. The resultant doubly protonated complex ((H,H) PDI)Al(OOCH)3 is the active catalyst for formic acid dehydrogenation. Given this, the catalytic cycle includes β-hydride elimination of ((H,H) PDI)Al(OOCH)3 to produce CO2, and the formed ((H,H) PDI)Al(OOCH)2 H mediates HCOOH to release H2. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Stereochemically probing the photo-Favorskii rearrangement: a mechanistic investigation.

PubMed

Givens, Richard S; Rubina, Marina; Stensrud, Kenneth F

2013-03-01

Using model (R)-2-acetyl-2-phenyl acetate esters of (S)- or (R)-α-substituted-p-hydroxybutyrophenones (S,R)-12a and (R,R)-12b, we have shown that a highly efficient photo-Favorskii rearrangement proceeds through a series of intermediates to form racemic rearrangement products. The stereogenic methine on the photoproduct, rac-2-(p-hydroxyphenyl)propanoic acid (rac-9), is formed by closure of a phenoxy-allyloxy intermediate 17 collapsing to a cyclopropanone, the "Favorskii" intermediate 18. These results quantify the intermediacy of a racemized triplet biradical (3)16 on the major rearrangement pathway elusively to the intermediate 18. Thus, intersystem crossing from the triplet biradical surface to the ground state generates a planar zwitterion prior to formation of a Favorskii cyclopropanone that retains no memory of its stereochemical origin. These results parallel the mechanism of Dewar and Bordwell for the ground state formation of cyclopropanone 3 that proceeds through an oxyallyl zwitterionic intermediate. The results are not consistent with the stereospecific S(N)2 ground state Favorskii mechanism observed by Stork, House, and Bernetti. Interconversion of the diastereomeric starting esters of (S,R)-12a and (R,R)-12b during photolysis did not occur, thus ruling out leaving group return prior to rearrangement.

Stereochemically Probing the photo-Favorskii Rearrangement: A Mechanistic Investigation

PubMed Central

Givens, Richard S.; Rubina, Marina; Stensrud, Kenneth F.

2012-01-01

Using model (R)-2-acetyl-2-phenyl acetate esters of (S)- or (R)-α-substituted-p-hydroxybutyrophenones (S,R)-12a and (R,R)-12b, we have shown that a highly efficient photo-Favorskii rearrangement proceeds through a series of intermediates to form racemic rearrangement products. The stereogenic methine on the photoproduct, rac-2-(p-hydroxyphenyl)propanoic acid (rac-9), is formed by closure of a phenoxy-allyloxy intermediate 17 collapsing to a cyclopropanone, the “Favorskii” intermediate 18. These results quantify the intermediacy of a racemized triplet biradical 316 on the major rearrangement pathway elusively to the intermediate 18. Thus, intersystem crossing from the triplet biradical surface to the ground state generates a planar zwitterion prior to formation of a Favorskii cyclopropanone that retains no memory of its stereochemical origin. These results parallel the mechanism of Dewar and Bordwell for the ground state formation of cyclopropanone 3 that proceed through an oxyallyl zwitterionic intermediate. The results are not consistent with the stereospecific SN2 ground state Favorskii mechanism observed by Stork, House, and Bernetti. Interconversion of the diastereomeric starting esters of (S,R)-12a and (R,R)-12b during photolysis did not occur thus ruling out leaving group return prior to rearrangement. PMID:23057737

Aryl Ketone Synthesis via Tandem Orthoplatinated Triarylphosphite-Catalyzed Addition Reactions of Arylboronic Acids with Aldehydes Followed by Oxidation

PubMed Central

Liao, Yuan-Xi; Hu, Qiao-Sheng

2010-01-01

Tandem orthoplatinated triarylphosphite-catalyzed addition reactions of arylboronic acids with aldehydes followed by oxidation to yield aryl ketones is described. 3-Pentanone was identified as a suitable oxidant for the tandem aryl ketone formation reaction. By using microwave energy, aryl ketones were obtained in high yields with the catalyst loading as low as 0.01%. PMID:20849092

Copper-catalyzed aerobic decarboxylative sulfonylation of cinnamic acids with sodium sulfinates: stereospecific synthesis of (E)-alkenyl sulfones.

PubMed

Jiang, Qing; Xu, Bin; Jia, Jing; Zhao, An; Zhao, Yu-Rou; Li, Ying-Ying; He, Na-Na; Guo, Can-Cheng

2014-08-15

A copper-catalyzed aerobic decarboxylative sulfonylation of alkenyl carboxylic acids with sodium sulfinates is developed. This study offers a new and expedient strategy for stereoselective synthesis of (E)-alkenyl sulfones that are widely present in biologically active natural products and therapeutic agents. Moreover, the transformation is proposed to proceed via a radical process and exhibits a broad substrate scope and good functional group tolerance.

Remarkable co-catalysis by copper(I) oxide in the palladium catalyzed cross-coupling of arylboronic acids with ethyl bromoacetate.

PubMed

Liu, Xing-xin; Deng, Min-zhi

2002-03-21

Copper(I) oxide can effectively co-catalyze the Suzuki type cross-coupling reactions of arylboronic acids with ethyl bromoacetate. As an alternative protocol for introducing the methylenecarboxy group into functionalized molecules, this reaction occurs in the absence of highly toxic thallium compounds or special ligands and should be convenient and practical.

Synthesis of fused tricyclic systems by thermal Cope rearrangement of furan-substituted vinyl cyclopropanes.

PubMed

Klaus, Verena; Wittmann, Stéphane; Senn, Hans M; Clark, J Stephen

2018-05-15

A novel method for the stereoselective construction of hexahydroazuleno[4,5-b]furans from simple precursors has been developed. The route involves the use of our recently developed Brønsted acid catalysed cyclisation reaction of acyclic ynenones to prepare fused 1-furanyl-2-alkenylcyclopropanes that undergo highly stereoselective thermal Cope rearrangement to produce fused tricyclic products. Substrates possessing an E-alkene undergo smooth Cope rearrangement at 40 °C, whereas the corresponding Z-isomers do not react at this temperature. Computational studies have been performed to explain the difference in behaviour of the E- and Z-isomers in the Cope rearrangement reaction. The hexahydroazuleno[4,5-b]furans produced by Cope rearrangement have potential as advanced intermediates for the synthesis of members of the guaianolide family of natural products.

Additional Nucleophile-Free FeCl3-Catalyzed Green Deprotection of 2,4-Dimethoxyphenylmethyl-Protected Alcohols and Carboxylic Acids.

PubMed

Sawama, Yoshinari; Masuda, Masahiro; Honda, Akie; Yokoyama, Hiroki; Park, Kwihwan; Yasukawa, Naoki; Monguchi, Yasunari; Sajiki, Hironao

2016-01-01

The deprotection of the methoxyphenylmethyl (MPM) ether and ester derivatives can be generally achieved by the combinatorial use of a catalytic Lewis acid and stoichiometric nucleophile. The deprotections of 2,4-dimethoxyphenylmethyl (DMPM)-protected alcohols and carboxylic acids were found to be effectively catalyzed by iron(III) chloride without any additional nucleophile to form the deprotected mother alcohols and carboxylic acids in excellent yields. Since the present deprotection proceeds via the self-assembling mechanism of the 2,4-DMPM protective group itself to give the hardly-soluble resorcinarene derivative as a precipitate, the rigorous purification process by silica-gel column chromatography was unnecessary and the sufficiently-pure alcohols and carboxylic acids were easily obtained in satisfactory yields after simple filtration.

A Highly Stereocontrolled, One-Pot Approach toward Pyrrolobenzoxazinones and Pyrroloquinazolinones through a Lewis Acid-Catalyzed [3 + 2]-Cycloannulation Process.

PubMed

Boomhoff, Michael; Ukis, Rostyslav; Schneider, Christoph

2015-08-21

We report herein a stereocontrolled [3 + 2]-cycloheteroannulation of bis-silyl dienediolate 1 with 2-aminobenzoic acid- and 2-aminobenzamide-derived imines to furnish highly substituted pyrrolo[1,2-a]benzoxazinones 3 and pyrrolo[1,2-a]quinazolinones 4, respectively, in good overall yields. This one-pot process rapidly generates molecular complexity and comprises a Lewis acid-catalyzed, vinylogous Mannich reaction of 1 followed by an intramolecular N,O-acetal- and N,N-aminal formation, respectively, which proceeds with good to excellent stereocontrol.

Hexose rearrangements upon fragmentation of N-glycopeptides and reductively aminated N-glycans.

PubMed

Wuhrer, Manfred; Koeleman, Carolien A M; Deelder, André M

2009-06-01

Tandem mass spectrometry of glycans and glycoconjugates in protonated form is known to result in rearrangement reactions leading to internal residue loss. Here we studied the occurrence of hexose rearrangements in tandem mass spectrometry of N-glycopeptides and reductively aminated N-glycans by MALDI-TOF/TOF-MS/MS and ESI-ion trap-MS/MS. Fragmentation of proton adducts of oligomannosidic N-glycans of ribonuclease B that were labeled with 2-aminobenzamide and 2-aminobenzoic acid resulted in transfer of one to five hexose residues to the fluorescently tagged innermost N-acetylglucosamine. Glycopeptides from various biological sources with oligomannosidic glycans were likewise shown to undergo hexose rearrangement reactions, resulting in chitobiose cleavage products that have acquired one or two hexose moieties. Tryptic immunoglobulin G Fc-glycopeptides with biantennary N-glycans likewise showed hexose rearrangements resulting in hexose transfer to the peptide moiety retaining the innermost N-acetylglucosamine. Thus, as a general phenomenon, tandem mass spectrometry of reductively aminated glycans as well as glycopeptides may result in hexose rearrangements. This characteristic of glycopeptide MS/MS has to be considered when developing tools for de novo glycopeptide structural analysis.

Improved Synthesis of 5-Substituted 1H-Tetrazoles via the [3+2] Cycloaddition of Nitriles and Sodium Azide Catalyzed by Silica Sulfuric Acid

PubMed Central

Du, Zhenting; Si, Changmei; Li, Youqiang; Wang, Yin; Lu, Jing

2012-01-01

A silica supported sulfuric acid catalyzed [3+2] cycloaddition of nitriles and sodium azide to form 5-substituted 1H-tetrazoles is described. The protocol can provide a series of 5-substituted 1H-tetrazoles using silica sulfuric acid from nitriles and sodium azide in DMF in 72%–95% yield. PMID:22606004

Acid-catalyzed hydrogenation during kerosene hydrodewaxing over H/ZSM-5

DOE Office of Scientific and Technical Information (OSTI.GOV)

Longstaff, D.C.; Hanson, F.V.

1996-11-01

Hydrogen addition to the products derived from cracking kerosene over H/ZSM-5 was observed at hydrogen pressures between 4.1-8.7 MPa and at 373-390{degrees}C. At low pressures, kerosene cracking over H/ZSM-5 yielded typical cracked products: aromatics, as well as low molecular weight saturates and olefins. Endothermic reactor temperature profiles were also observed, indicative of cracking reactions. At high hydrogen partial pressures product selectivity was altered in that kerosene cracking gave high yields of low molecular weight paraffins and low yields of olefins and aromatics. Reactor temperature profiles were exothermic, indicative of hydrocracking reactions. A mechanism for acid catalyzed hydrogenation is suggested. Althoughmore » hydrogenation was not observed at lower hydrogen pressures, hydrogen proved beneficial in maintaining catalyst activity at a stable level. Lost catalyst activity was restored by maintaining the catalyst under static hydrogen at 1.4 MPa and 370{degrees}C for 16h. 36 refs., 14 figs., 3 tabs.« less

Dynamic Kinetic Resolution of Allylic Sulfoxides by Rh-Catalyzed Hydrogenation: A Combined Theoretical and Experimental Mechanistic Study

PubMed Central

Dornan, Peter K.; Kou, Kevin G. M.; Houk, K. N.; Dong, Vy M.

2014-01-01

A dynamic kinetic resolution (DKR) of allylic sulfoxides has been demonstrated by combining the Mislow [2,3]-sigmatropic rearrangement with catalytic asymmetric hydrogenation. The efficiency of our DKR was optimized by using low pressures of hydrogen gas to decrease the rate of hydrogenation relative to the rate of sigmatropic rearrangement. Kinetic studies reveal that the rhodium complex acts as a dual-role catalyst and accelerates the substrate racemization while catalyzing olefin hydrogenation. Scrambling experiments and theoretical modeling support a novel mode of sulfoxide racemization which occurs via a rhodium π-allyl intermediate in polar solvents. In non-polar solvents, however, the substrate racemization is primarily uncatalyzed. Computational studies suggest that the sulfoxide binds to rhodium via O–coordination throughout the catalytic cycle for hydrogenation. PMID:24350903

Selective Formation of Secondary Amides via the Copper-Catalyzed Cross-Coupling of Alkylboronic Acids with Primary Amides

PubMed Central

Rossi, Steven A.; Shimkin, Kirk W.; Xu, Qun; Mori-Quiroz, Luis M.; Watson, Donald A.

2014-01-01

For the first time, a general catalytic procedure for the cross coupling of primary amides and alkylboronic acids is demonstrated. The key to the success of this reaction was the identification of a mild base (NaOSiMe3) and oxidant (di-tert-butyl peroxide) to promote the copper-catalyzed reaction in high yield. This transformation provides a facile, high-yielding method for the mono-alkylation of amides. PMID:23611591

Unexpected Catalytic Reactions of Silyl-protected Enoldiazoacetates With Nitrile Oxides That Form 5- Arylaminofuran-2(3H)-one-4-carboxylates

PubMed Central

Xu, Xinfang; Shabashov, Dmitry; Zavalij, Peter Y.; Doyle, Michael P.

2012-01-01

Silyl-protected enoldiazoacetates undergo dirhodium(II) catalyzed reactions with nitrile oxides to form acid-labile ketenimines via dipolar cycloaddition of nitrile oxides to a donor/acceptor cyclopropene and Lossen rearrangement of the dipolar adduct; acid catalysis converts the ketenimine to the furan product. PMID:22272728

Cu-catalyzed formal methylative and hydrogenative carboxylation of alkynes with carbon dioxide: efficient synthesis of α,β-unsaturated carboxylic acids.

PubMed

Takimoto, Masanori; Hou, Zhaomin

2013-08-19

The sequential hydroalumination or methylalumination of various alkynes catalyzed by different catalyst systems, such those based on Sc, Zr, and Ni complexes, and the subsequent carboxylation of the resulting alkenylaluminum species with CO2 catalyzed by an N-heterocyclic carbene (NHC)-copper catalyst have been examined in detail. The regio- and stereoselectivity of the overall reaction relied largely on the hydroalumination or methylalumination reactions, which significantly depended on the catalyst and alkyne substrates. The subsequent Cu-catalyzed carboxylation proceeded with retention of the stereoconfiguration of the alkenylaluminum species. All the reactions could be carried out in one-pot to afford efficiently a variety of α,β-unsaturated carboxylic acids with well-controlled configurations, which are difficult to construct by previously reported methods. This protocol could be practically useful and attractive because of its high regio- and stereoselectivity, simple one-pot reaction operation, and the use of CO2 as a starting material. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Palladium-Catalyzed Asymmetric Allylic Alkylation of 4-Substituted Isoxazolidin-5-ones: Straightforward Access to β2,2 -Amino Acids.

PubMed

Nascimento de Oliveira, Marllon; Arseniyadis, Stellios; Cossy, Janine

2018-04-03

We report here an unprecedented and highly enantioselective palladium-catalyzed allylic alkylation applied to 4-substituted isoxazolidin-5-ones. Ultimately, the process provides a straightforward access to β 2,2 -amino acids bearing an all-carbon quaternary stereogenic center in great yields and a high degree of enantioselectivity. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Asymmetric synthesis of all-carbon benzylic quaternary stereocenters via Cu-catalyzed conjugate addition of dialkylzinc reagents to 5-(1-arylalkylidene) Meldrum's acids.

PubMed

Fillion, Eric; Wilsily, Ashraf

2006-03-08

The asymmetric synthesis of all-carbon benzylic quaternary stereocenters has been successfully achieved through copper-catalyzed addition of dialkylzinc reagents to 5-(1-arylalkylidene) and 5-(dihydroindenylidene) Meldrum's acids in the presence of phosphoramidite ligand. The resulting benzyl-substituted Meldrum's acids and 1,1-disubstituted indanes were obtained in good yields and up to 99% ee. The significance of substituting the position para, meta, and ortho to the electrophilic benzylic center was highlighted. A benzyl Meldrum's acid product was further transformed to a 3,3-disubstituted 1-indanone and a beta,beta-disubstituted pentanoic acid.

Characterization of a Cross-Linked Protein–Nucleic Acid Substrate Radical in the Reaction Catalyzed by RlmN

PubMed Central

2015-01-01

RlmN and Cfr are methyltransferases/methylsynthases that belong to the radical S-adenosylmethionine superfamily of enzymes. RlmN catalyzes C2 methylation of adenosine 2503 (A2503) of 23S rRNA, while Cfr catalyzes C8 methylation of the exact same nucleotide, and will subsequently catalyze C2 methylation if the site is unmethylated. A key feature of the unusual mechanisms of catalysis proposed for these enzymes is the attack of a methylene radical, derived from a methylcysteine residue, onto the carbon center undergoing methylation to generate a paramagnetic protein–nucleic acid cross-linked species. This species has been thoroughly characterized during Cfr-dependent C8 methylation, but does not accumulate to detectible levels in RlmN-dependent C2 methylation. Herein, we show that inactive C118S/A variants of RlmN accumulate a substrate-derived paramagnetic species. Characterization of this species by electron paramagnetic resonance spectroscopy in concert with strategic isotopic labeling shows that the radical is delocalized throughout the adenine ring of A2503, although predominant spin density is on N1 and N3. Moreover, 13C hyperfine interactions between the radical and the methylene carbon of the formerly [methyl-13C]Cys355 residue show that the radical species exists in a covalent cross-link between the protein and the nucleic acid substrate. X-ray structures of RlmN C118A show that, in the presence of SAM, the substitution does not alter the active site structure compared to that of the wild-type enzyme. Together, these findings have new mechanistic implications for the role(s) of C118 and its counterpart in Cfr (C105) in catalysis, and suggest involvement of the residue in resolution of the cross-linked species via a radical mediated process. PMID:24806349

Characterization of a Cross-Linked Protein-Nucleic Acid Substrate Radical in the Reaction Catalyzed by RlmN

DOE Office of Scientific and Technical Information (OSTI.GOV)

Silakov, Alexey; Grove, Tyler L.; Radle, Matthew I.

2014-08-14

RlmN and Cfr are methyltransferases/methylsynthases that belong to the radical S-adenosylmethionine superfamily of enzymes. RlmN catalyzes C2 methylation of adenosine 2503 (A2503) of 23S rRNA, while Cfr catalyzes C8 methylation of the exact same nucleotide, and will subsequently catalyze C2 methylation if the site is unmethylated. A key feature of the unusual mechanisms of catalysis proposed for these enzymes is the attack of a methylene radical, derived from a methylcysteine residue, onto the carbon center undergoing methylation to generate a paramagnetic protein–nucleic acid cross-linked species. This species has been thoroughly characterized during Cfr-dependent C8 methylation, but does not accumulate tomore » detectible levels in RlmN-dependent C2 methylation. Herein, we show that inactive C118S/A variants of RlmN accumulate a substrate-derived paramagnetic species. Characterization of this species by electron paramagnetic resonance spectroscopy in concert with strategic isotopic labeling shows that the radical is delocalized throughout the adenine ring of A2503, although predominant spin density is on N1 and N3. Moreover, 13C hyperfine interactions between the radical and the methylene carbon of the formerly [methyl- 13C]Cys355 residue show that the radical species exists in a covalent cross-link between the protein and the nucleic acid substrate. X-ray structures of RlmN C118A show that, in the presence of SAM, the substitution does not alter the active site structure compared to that of the wild-type enzyme. Together, these findings have new mechanistic implications for the role(s) of C118 and its counterpart in Cfr (C105) in catalysis, and suggest involvement of the residue in resolution of the cross-linked species via a radical mediated process« less

Catalytic synthesis of amides via aldoximes rearrangement.

PubMed

Crochet, Pascale; Cadierno, Victorio

2015-02-14

Amide bond formation reactions are among the most important transformations in organic chemistry because of the widespread occurrence of amides in pharmaceuticals, natural products and biologically active compounds. The Beckmann rearrangement is a well-known method to generate secondary amides from ketoximes. However, under the acidic conditions commonly employed, aldoximes RHC=NOH rarely rearrange into the corresponding primary amides RC(=O)NH2. In recent years, it was demonstrated that this atom-economical transformation can be carried out efficiently and selectively with the help of metal catalysts. Several homogeneous and heterogenous systems have been described. In addition, protocols offering the option to generate the aldoximes in situ from the corresponding aldehydes and hydroxylamine, or even from alcohols, have also been developed, as well as a series of tandem processes allowing the access to N-substituted amide products. In this Feature article a comprehensive overview of the advances achieved in this particular research area is presented.

Characterization and optimization of carboxylesterase-catalyzed esterification between capric acid and glycerol for the production of 1-monocaprin in reversed micellar system.

PubMed

Park, Kyung Min; Kwon, Oh Taek; Ahn, Seon Min; Lee, JaeHwan; Chang, Pahn-Shick

2010-02-28

Calotropis procera R. Br. carboxylesterase (EC 3.1.1.1) solubilized in reversed micellar glycerol droplets containing a very small amount of water (less than 5ppm) and stabilized by a surfactant effectively catalyzed the esterification between glycerol and capric acid to produce 1-monocaprin. Reaction variables including surfactant types, organic solvent media, reaction time, G-value ([glycerol]/[capric acid]), R-value ([water]/[surfactant]), pH, temperature, and types of metal ion inhibitors on the carboxylesterase-catalyzed esterification were characterized and optimized to efficiently produce 1-monocaprin. Bis(2-ethylhexyl) sodium sulfosuccinate (AOT) and isooctane were the most effective surfactant and organic solvent medium, respectively, for 1-monocaprin formation in reversed micelles. The optimum G- and R-values were 3.0 and 0.05, respectively, and the optimum pH and temperature were determined to be 10.0 and 60 degrees C, respectively. K(m,app.) and V(max,app.) were calculated from a Hanes-Woolf plot, and the values were 9.64 mM and 2.45 microM/min mg protein, respectively. Among various metal ions, Cu(2+) and Fe(2+) severely inhibited carboxylesterase-catalyzed esterification activity (less than 6.0% of relative activity). Copyright 2009 Elsevier B.V. All rights reserved.

A: The Progression of a Catalytic Immune Response. B: Molecular Recognition of Anions by Silica Bound Sapphyrin

DTIC Science & Technology

1994-08-01

Diels - Alder reactions (58-60), Claisen rearrangements (43-45), olefin isomerization (73), a O-elimination (74), an asymmetric ketone reduction (54...phosphorothioate hapten3 ........ 19 Figure 5. Carboxylic acid hydrolysis .................... 21 Figure 6. Reaction coordinates for antibody catalyzed ...and catalyze the reaction. Thus, it is important to design transition analogs that closely mimic the transition state in every possible chemical

Nickel-Catalyzed Coupling of Alkenes, Aldehydes, and Silyl Triflates

PubMed Central

Ng, Sze-sze; Ho, Chun-Yu; Jamison, Timothy F.

2011-01-01

A full account of two recently developed nickel-catalyzed coupling reactions of alkenes, aldehydes and silyl triflates is presented. These reactions provide either allylic alcohol or homoallylic alcohol derivatives selectively, depending on the ligand employed. These processes are believed to be mechanistically distinct from Lewis acid-catalyzed carbonyl-ene reactions, and several lines of evidence supporting this hypothesis are discussed. PMID:16939275

Autoxidative and Cyclooxygenase-2 Catalyzed Transformation of the Dietary Chemopreventive Agent Curcumin*

PubMed Central

Griesser, Markus; Pistis, Valentina; Suzuki, Takashi; Tejera, Noemi; Pratt, Derek A.; Schneider, Claus

2011-01-01

The efficacy of the diphenol curcumin as a cancer chemopreventive agent is limited by its chemical and metabolic instability. Non-enzymatic degradation has been described to yield vanillin, ferulic acid, and feruloylmethane through cleavage of the heptadienone chain connecting the phenolic rings. Here we provide evidence for an alternative mechanism, resulting in autoxidative cyclization of the heptadienone moiety as a major pathway of degradation. Autoxidative transformation of curcumin was pH-dependent with the highest rate at pH 8 (2.2 μm/min) and associated with stoichiometric uptake of O2. Oxidation was also catalyzed by recombinant cyclooxygenase-2 (COX-2) (50 nm; 7.5 μm/min), and the rate was increased ≈10-fold by the addition of 300 μm H2O2. The COX-2 catalyzed transformation was inhibited by acetaminophen but not indomethacin, suggesting catalysis occurred by the peroxidase activity. We propose a mechanism of enzymatic or autoxidative hydrogen abstraction from a phenolic hydroxyl to give a quinone methide and a delocalized radical in the heptadienone chain that undergoes 5-exo cyclization and oxygenation. Hydration of the quinone methide (measured by the incorporation of O-18 from H218O) and rearrangement under loss of water gives the final dioxygenated bicyclopentadione product. When curcumin was added to RAW264.7 cells, the bicyclopentadione was increased 1.8-fold in cells activated by LPS; vanillin and other putative cleavage products were negligible. Oxidation to a reactive quinone methide is the mechanistic basis of many phenolic anti-cancer drugs. It is possible, therefore, that oxidative transformation of curcumin, a prominent but previously unrecognized reaction, contributes to its cancer chemopreventive activity. PMID:21071447

Unexpected catalytic reactions of silyl-protected enol diazoacetates with nitrile oxides that form 5-arylaminofuran-2(3H)-one-4-carboxylates.

PubMed

Xu, Xinfang; Shabashov, Dmitry; Zavalij, Peter Y; Doyle, Michael P

2012-02-03

Silyl-protected enol diazoacetates undergo dirhodium(II)-catalyzed reactions with nitrile oxides to form acid-labile ketenimines via dipolar cycloaddition of nitrile oxides to a donor/acceptor cyclopropene and Lossen rearrangement of the dipolar adduct; acid catalysis converts the ketenimine to the furan product. © 2012 American Chemical Society

Finding local genome rearrangements.

PubMed

Simonaitis, Pijus; Swenson, Krister M

2018-01-01

The double cut and join (DCJ) model of genome rearrangement is well studied due to its mathematical simplicity and power to account for the many events that transform gene order. These studies have mostly been devoted to the understanding of minimum length scenarios transforming one genome into another. In this paper we search instead for rearrangement scenarios that minimize the number of rearrangements whose breakpoints are unlikely due to some biological criteria. One such criterion has recently become accessible due to the advent of the Hi-C experiment, facilitating the study of 3D spacial distance between breakpoint regions. We establish a link between the minimum number of unlikely rearrangements required by a scenario and the problem of finding a maximum edge-disjoint cycle packing on a certain transformed version of the adjacency graph. This link leads to a 3/2-approximation as well as an exact integer linear programming formulation for our problem, which we prove to be NP-complete. We also present experimental results on fruit flies, showing that Hi-C data is informative when used as a criterion for rearrangements. A new variant of the weighted DCJ distance problem is addressed that ignores scenario length in its objective function. A solution to this problem provides a lower bound on the number of unlikely moves necessary when transforming one gene order into another. This lower bound aids in the study of rearrangement scenarios with respect to chromatin structure, and could eventually be used in the design of a fixed parameter algorithm with a more general objective function.

BAMBERGER REARRANGEMENT DURING TNT-METABOLISM BY CLOSTRIDIUM ACETORBUTYLICUM. (R825513C006)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

An Iterative O-Methyltransferase Catalyzes 1,11-Dimethylation of Aspergillus fumigatus Fumaric Acid Amides.

PubMed

Kalb, Daniel; Heinekamp, Thorsten; Schieferdecker, Sebastian; Nett, Markus; Brakhage, Axel A; Hoffmeister, Dirk

2016-10-04

S-adenosyl-l-methionine (SAM)-dependent methyltransfer is a common biosynthetic strategy to modify natural products. We investigated the previously uncharacterized Aspergillus fumigatus methyltransferase FtpM, which is encoded next to the bimodular fumaric acid amide synthetase FtpA. Structure elucidation of two new A. fumigatus natural products, the 1,11-dimethyl esters of fumaryl-l-tyrosine and fumaryl-l-phenylalanine, together with ftpM gene disruption suggested that FtpM catalyzes iterative methylation. Final evidence that a single enzyme repeatedly acts on fumaric acid amides came from an in vitro biochemical investigation with recombinantly produced FtpM. Size-exclusion chromatography indicated that this methyltransferase is active as a dimer. As ftpA and ftpM homologues are found clustered in other fungi, we expect our work will help to identify and annotate natural product biosynthesis genes in various species. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Acid-catalyzed conversion of mono- and poly-sugars into platform chemicals: effects of molecular structure of sugar substrate.

PubMed

Hu, Xun; Wu, Liping; Wang, Yi; Song, Yao; Mourant, Daniel; Gunawan, Richard; Gholizadeh, Mortaza; Li, Chun-Zhu

2013-04-01

Hydrolysis/pyrolysis of lignocellulosic biomass always produces a mixture of sugars with distinct structures as intermediates or products. This study tried to elucidate the effects of molecular structure of sugars on their acid-catalyzed conversions in ethanol/water. Location of carbonyl group in sugars (fructose versus glucose) and steric configuration of hydroxyl groups (glucose versus galactose) significantly affected yields of levulinic acid/ester (fructose>glucose>galactose). The dehydration of fructose to 5-(hydroxymethyl)furfural produces much less soluble polymer than that from glucose and galactose, which results in high yields of levulinic acid/ester from fructose. Anhydrate sugar such as levoglucosan tends to undergo the undesirable decomposition to form less levulinic acid/ester. Catalytic behaviors of the poly-sugars (sucrose, maltose, raffinose, β-cyclodextrins) were determined much by their basic units. However, their big molecular sizes create the steric hindrance that significantly affects their followed conversion over solid acid catalyst. Copyright © 2013 Elsevier Ltd. All rights reserved.

Sequence dependent N-terminal rearrangement and degradation of peptide nucleic acid (PNA) in aqueous solution

NASA Technical Reports Server (NTRS)

Eriksson, M.; Christensen, L.; Schmidt, J.; Haaima, G.; Orgel, L.; Nielsen, P. E.

1998-01-01

The stability of the PNA (peptide nucleic acid) thymine monomer inverted question markN-[2-(thymin-1-ylacetyl)]-N-(2-aminoaminoethyl)glycine inverted question mark and those of various PNA oligomers (5-8-mers) have been measured at room temperature (20 degrees C) as a function of pH. The thymine monomer undergoes N-acyl transfer rearrangement with a half-life of 34 days at pH 11 as analyzed by 1H NMR; and two reactions, the N-acyl transfer and a sequential degradation, are found by HPLC analysis to occur at measurable rates for the oligomers at pH 9 or above. Dependent on the amino-terminal sequence, half-lives of 350 h to 163 days were found at pH 9. At pH 12 the half-lives ranged from 1.5 h to 21 days. The results are discussed in terms of PNA as a gene therapeutic drug as well as a possible prebiotic genetic material.

Mechanistic insights into iron catalyzed dehydrogenation of formic acid: β-hydride elimination vs. direct hydride transfer.

PubMed

Yang, Xinzheng

2013-09-07

Density functional theory calculations reveal a complete reaction mechanism with detailed energy profiles and transition state structures for the dehydrogenation of formic acid catalyzed by an iron complex, [P(CH2CH2PPh2)3FeH](+). In the cationic reaction pathway, a β-hydride elimination process is confirmed to be the rate-determining step in this catalytic reaction. A potential reaction pathway starting with a direct hydride transfer from HCOO(-) to Fe is found to be possible, but slightly less favorable than the catalytic cycle with a β-hydride elimination step.

Brönsted Acid-Catalyzed One-Pot Synthesis of Indoles from o-Aminobenzyl Alcohols and Furans

PubMed Central

Kuznetsov, Alexey; Makarov, Anton; Rubtsov, Alexandr E.; Butin, Alexander V.; Gevorgyan, Vladimir

2013-01-01

Brönsted acid-catalyzed one-pot synthesis of indoles from o-aminobenzyl alcohols and furans has been developed. This method operates via the in situ formation of aminobenzylfuran, followed by its recyclization into the indole core. The method proved to be efficient for substrates possessing different functional groups, including -OMe, -CO2Cy, and -Br. The resulting indoles can easily be transformed into diverse scaffolds, including 2,3- and 1,2-fused indoles, and indole possessing an α,β-unsaturated ketone moiety at the C-2 position. PMID:24255969

Roles of the Lewis acid and base in the chemical reduction of CO2 catalyzed by frustrated Lewis pairs.

PubMed

Lim, Chern-Hooi; Holder, Aaron M; Hynes, James T; Musgrave, Charles B

2013-09-03

We employ quantum chemical calculations to discover how frustrated Lewis pairs (FLP) catalyze the reduction of CO2 by ammonia borane (AB); specifically, we examine how the Lewis acid (LA) and Lewis base (LB) of an FLP activate CO2 for reduction. We find that the LA (trichloroaluminum, AlCl3) alone catalyzes hydride transfer (HT) to CO2 while the LB (trimesitylenephosphine, PMes3) actually hinders HT; inclusion of the LB increases the HT barrier by ∼8 kcal/mol relative to the reaction catalyzed by LAs only. The LB hinders HT by donating its lone pair to the LUMO of CO2, increasing the electron density on the C atom and thus lowering its hydride affinity. Although the LB hinders HT, it nonetheless plays a crucial role by stabilizing the active FLP·CO2 complex relative to the LA dimer, free CO2, and free LB. This greatly increases the concentration of the reactive complex in the form FLP·CO2 and thus increases the rate of reaction. We expect that the principles we describe will aid in understanding other catalytic CO2 reductions.

Development of a Lewis Base Catalyzed Selenocyclization Reaction

ERIC Educational Resources Information Center

Collins, William

2009-01-01

The concept of Lewis base activation of selenium Lewis acids has been effectively reduced to practice in the Lewis base catalyzed selenofunctionalization of unactivated olefins. In this reaction, the weakly acidic species, "N"-phenylselenyl succinimide, is cooperatively activated by the addition of a "soft" Lewis base donor (phosphine sulfides,…

Mechanistic Study on Cu(II)-Catalyzed Oxidative Cross-Coupling Reaction between Arenes and Boronic Acids under Aerobic Conditions.

PubMed

Zhang, Qian; Liu, Yang; Wang, Ting; Zhang, Xinhao; Long, Chao; Wu, Yun-Dong; Wang, Mei-Xiang

2018-04-25

Substantial attention has been given to modern organocopper chemistry in recent years since copper salts are naturally abundant, cheap, and less toxic in comparison to precious metals. Copper salts also exhibit versatility in catalyzing and mediating carbon-carbon and carbon-heteroatom bond forming reactions. Despite the wide applications of copper salts in catalysis, reaction mechanisms have remained elusive. Using azacalix[1]arene[3]pyridine, an arene-embedded macrocycle, and its isolated and structurally well-defined ArCu(II) and ArCu(III) compounds as molecular tools, we now report an in-depth experimental and computational study on the mechanism of a Cu(II)-catalyzed oxidative cross-coupling reaction between arenes and boronic acids with air as the oxidant. Stoichiometric reaction of organocopper compounds with p-tolylboronic acid validated arylcopper(II) rather than arylcopper(III) as a reactive organometallic intermediate. XPS, EPR, 1 H NMR, HRMS, and UV-vis spectroscopic evidence along with the isolation and quantification of all products and copper speciation, combined with computational analysis of the electronic structure and energetics of the transient intermediates, suggested a reaction sequence involving electrophilic metalation of arene by Cu(II), transmetalation of arylboronate to ArCu(II), the redox reaction between the resulting ArCu(II)Ar' and ArCu(II) to form respectively ArCu(III)Ar' and ArCu(I), and finally reductive elimination of ArCu(III)Ar'. Under aerobic catalytic conditions, all Cu(I) ions released from reductive elimination of ArCu(III)Ar' and from protolysis of ArCu(I) were oxidized by oxygen to regenerate Cu(II) species that enters into the next catalytic cycle. The unraveled reactivity of arylcopper(II) compounds and the catalytic cycle would enrich our knowledge of modern organocopper chemistry and provide useful information in the design of copper-catalyzed reactions.

Recovery of slaughterhouse Animal Fatty Wastewater Sludge by conversion into Fatty Acid Butyl Esters by acid-catalyzed esterification.

PubMed

Wallis, Christopher; Cerny, Muriel; Lacroux, Eric; Mouloungui, Zéphirin

2017-02-01

Two types of Animal Fatty Wastewater Sludges (AFWS 1 and 2) were analyzed and fully characterized to determine their suitability for conversion into biofuel. AFWS 1 was determined to be unsuitable as it contains 68.8wt.% water and only 32.3wt.% dry material, of which only around 80% is lipids to be converted. AFWS 2 has only 15.7wt.% water and 84.3wt.% dry material of which is assumed to 100% lipids as the protein and ash contents were determined to be negligible. The 4-dodecylbenzenesulfonic acid (DBSA) catalyzed esterification of AFWS with 1-butanol was performed in a novel batch reactor fitted with a drying chimney for the "in situ" removal of water and optimized using a non-conventional Doehlert surface response methodology. The optimized condition was found to be 1.66mol equivalent of 1-butanol (with respect to total fatty acid chains), 10wt.% of DBSA catalyst (with respect to AFWS) at 105°C for 3h. Fatty Acid Butyl Esters (FABEs) were isolated in good yields (95%+) as well as a blend of FABEs with 1-butanol (16%). The two potential biofuels were analyzed in comparison with current and analogous biofuels (FAME based biodiesel, and FABE products made from vegetable oils) and were found to exhibit high cetane numbers and flash point values. Copyright © 2016 Elsevier Ltd. All rights reserved.

Rhodium-Catalyzed Dehydrogenative Borylation of Cyclic Alkenes

PubMed Central

Kondoh, Azusa; Jamison, Timothy F.

2010-01-01

A rhodium-catalyzed dehydrogenative borylation of cyclic alkenes is described. This reaction provides direct access to cyclic 1-alkenylboronic acid pinacol esters, useful intermediates in organic synthesis. Suzuki-Miyaura cross-coupling applications are also presented. PMID:20107646

Peroxygenase-Catalyzed Fatty Acid Epoxidation in Cereal Seeds (Sequential Oxidation of Linoleic Acid into 9(S),12(S),13(S)-Trihydroxy-10(E)-Octadecenoic Acid).

PubMed Central

Hamberg, M.; Hamberg, G.

1996-01-01

Peroxygenase-catalyzed epoxidation of oleic acid in preparations of cereal seeds was investigated. The 105,000g particle fraction of oat (Avena sativa) seed homogenate showed high peroxygenase activity, i.e. 3034 [plus or minus] 288 and 2441 [plus or minus] 168 nmol (10 min)-1 mg-1 protein in two cultivars, whereas the corresponding fraction obtained from barley (Hordeum vulgare and Hordeum distichum), rye (Secale cereale), and wheat (Triticum aestivum) showed only weak activity, i.e. 13 to 138 nmol (10 min)-1 mg-1 protein. In subcellular fractions of oat seed homogenate, peroxygenase specific activity was highest in the 105,000g particle fraction, whereas lipoxygenase activity was more evenly distributed and highest in the 105,000g supernatant fraction. Incubation of [1-14C]linoleic acid with the 105,000g supernatant of oat seed homogenate led to the formation of several metabolites, i.e. in order of decreasing abundance, 9(S)-hydroxy-10(E),12(Z)-octadecadienoic acid, 9(S),12(S),13(S)-trihydroxy-10(E)-octadecenoic acid, cis-9,10-epoxy-12(Z)-octadecenoic acid [mainly the 9(R),10(S) enantiomer], cis-12,13-epoxy-9(Z)-octadecenoic acid [mainly the 12(R),13(S) enantiomer], threo-12,13-dihydroxy-9(Z)-octadecenoic acid, and 12(R),13(S)-epoxy-9(S)-hydroxy-10(E)-octadecenoic acid. Incubation of linoleic acid with the 105,000g particle fraction gave a similar, but not identical, pattern of metabolites. Conversion of linoleic acid into 9(S),12(S),13(S)-trihydroxy-10(E)-octadecenoic acid, a naturally occurring oxylipin with antifungal properties, took place by a pathway involving sequential catalysis by lipoxygenase, peroxygenase, and epoxide hydrolase. PMID:12226220

Ultra-sensitive EUV resists based on acid-catalyzed polymer backbone breaking

NASA Astrophysics Data System (ADS)

Manouras, Theodoros; Kazazis, Dimitrios; Koufakis, Eleftherios; Ekinci, Yasin; Vamvakaki, Maria; Argitis, Panagiotis

2018-03-01

The main target of the current work was to develop new sensitive polymeric materials for lithographic applications, focusing in particular to EUV lithography, the main chain of which is cleaved under the influence of photogenerated acid. Resist materials based on the cleavage of polymer main chain are in principle capable to create very small structures, to the dimensions of the monomers that they consist of. Nevertheless, in the case of the commonly used nonchemically amplified materials of this type issues like sensitivity and poor etch resistance limit their areas of application, whereas inadequate etch resistance and non- satisfactory process reliability are the usual problems encountered in acid catalysed materials based on main chain scission. In our material design the acid catalyzed chain cleavable polymers contain very sensitive moieties in their backbone while they remain intact in alkaline ambient. These newly synthesized polymers bear in addition suitable functional groups for the achievement of desirable lithographic characteristics (thermal stability, acceptable glass transition temperature, etch resistance, proper dissolution behavior, adhesion to the substrate). Our approach for achieving acceptable etch resistance, a main drawback in other main chain cleavable resists, is based on the introduction of polyaromatic hydrocarbons in the polymeric backbone, whereas the incorporation of an inorganic component further enhances the etch resistance. Single component systems can also be designed following the proposed approach by the incorporation of suitable PAGs and base quencher molecules in the main chain. Resist formulations based on a random copolymer designed according to the described rules evaluated in EUV exhibit ultrahigh sensitivity, capability for high resolution patterning and overall processing characteristics that make them strong candidates for industrial use upon further optimization.

Chromosome-specific staining to detect genetic rearrangements associated with chromosome 3 and/or chromosome 17

DOEpatents

Gray, Joe W.; Pinkel, Daniel; Kallioniemi, Olli-Pekka; Kallioniemi, Anne; Sakamoto, Masaru

2002-01-01

Methods and compositions for staining based upon nucleic acid sequence that employ nudeic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyses. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods and reagents are provided for the detection of genetic rearrangements. Probes and test kits are provided for use in detecting genetic rearrangements, particularly for use in tumor cytogenetics, in the detection of disease related loci, specifically cancer, such as chronic myelogenous leukemia (CML), retinoblastoma, ovarian and uterine cancers, and for biological dosimetry. Methods and reagents are described for cytogenetic research, for the differentiation of cytogenetically similar but genetically different diseases, and for many prognostic and diagnostic applications.

Chromosome-specific staining to detect genetic rearrangements associated with chromosome 3 and/or chromosome 17

DOEpatents

Gray, Joe W.; Pinkel, Daniel; Kallioniemi, Olli-Pekka; Kallioniemi, Anne; Sakamoto, Masaru

2008-09-09

Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyses. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods and reagents are provided for the detection of genetic rearrangements. Probes and test kits are provided for use in detecting genetic rearrangements, particularly for use in tumor cytogenetics, in the detection of disease related loci, specifically cancer, such as chronic myelogenous leukemia (CML), retinoblastoma, ovarian and uterine cancers, and for biological dosimetry. Methods and reagents are described for cytogenetic research, for the differentiation of cytogenetically similar but genetically different diseases, and for many prognostic and diagnostic applications.

Chromosome-specific staining to detect genetic rearrangements associated with chromosome 3 and/or chromosome 17

DOEpatents

Gray, Joe W [San Francisco, CA; Pinkel, Daniel [Lafayette, CA; Kallioniemi, Olli-Pekka [Turku, FI; Kallioniemi, Anne [Tampere, FI; Sakamoto, Masaru [Tokyo, JP

2009-10-06

Methods and compositions for staining based upon nucleic acid sequence that employ .[.nudeic.]. .Iadd.nucleic .Iaddend.acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyses. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods and reagents are provided for the detection of genetic rearrangements. Probes and test kits are provided for use in detecting genetic rearrangements, particularly for use in tumor cytogenetics, in the detection of disease related loci, specifically cancer, such as chronic myelogenous leukemia (CML), retinoblastoma, ovarian and uterine cancers, and for biological dosimetry. Methods and reagents are described for cytogenetic research, for the differentiation of cytogenetically similar but genetically different diseases, and for many prognostic and diagnostic applications.

Chromosome-Specific Staining To Detect Genetic Rearrangements Associated With Chromosome 3 And/Or Chromosone 17

DOEpatents

Gray; Joe W.; Pinkel; Daniel; Kallioniemi; Olli-Pekka; Kallioniemi; Anne; Sakamoto; Masaru

2002-02-05

Methods and compositions for staining based upon nucleic acid sequence that employ nucleic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyses. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods and reagents are provided for the detection of genetic rearrangements. Probes and test kits are provided for use in detecting genetic rearrangements, particularly for use in tumor cytogenetics, in the detection of disease related loci, specifically cancer, such as chronic myelogenous leukemia (CML), retinoblastoma, ovarian and uterine cancers, and for biological dosimetry. Methods and reagents are described for cytogenetic research, for the differentiation of cytogenetically similar but genetically different diseases, and for many prognostic and diagnostic applications.

Degradations and Rearrangement Reactions

NASA Astrophysics Data System (ADS)

Zhang, Jianbo

This section deals with recent reports concerning degradation and rearrangement reactions of free sugars as well as some glycosides. The transformations are classified in chemical and enzymatic ways. In addition, the Maillard reaction will be discussed as an example of degradation and rearrangement transformation and its application in current research in the fields of chemistry and biology.

Iridium-Catalyzed Asymmetric Hydrogenation of Ketones with Accessible and Modular Ferrocene-Based Amino-phosphine Acid (f-Ampha) Ligands.

PubMed

Yu, Jianfei; Long, Jiao; Yang, Yuhong; Wu, Weilong; Xue, Peng; Chung, Lung Wa; Dong, Xiu-Qin; Zhang, Xumu

2017-02-03

A series of tridentate ferrocene-based amino-phosphine acid (f-Ampha) ligands have been successfully developed. The f-Ampha ligands are extremely air stable and exhibited excellent performance in the Ir-catalyzed asymmetric hydrogenation of ketones (full conversions, up to >99% ee, and 500 000 TON). DFT calculations were performed to elucidate the reaction mechanism and the importance of the -COOH group. Control experiments also revealed that the -COOH group played a key role in this reaction.

Triphenylphosphine as Ligand for Room Temperature Ni(0)-Catalyzed Cross-Coupling Reactions of Aryl Chlorides with Arylboronic Acids

PubMed Central

Tang, Zhen-Yu; Hu, Qiao-Sheng

2008-01-01

Room temperature Ni(0)-catalyzed cross-coupling reactions of deactivated aryl chlorides with arylboronic acids with inexpensive triphenylphosphine (PPh3) as a supporting ligand have been accomplished in good to excellent yields. Air-stable Ni(PPh3)2Cl2 has also been established as catalyst precursor and highly active nickel catalysts were obtained when the reduction of Ni(PPh3)2Cl2 with n-BuLi was carried out in presence of an aryl chloride. PMID:16497011

Lipase-catalyzed production of short-chain acids terpenyl esters of interest to the food industry.

PubMed

Laboret, F; Perraud, R

1999-12-01

The production of low molecular weight esters as flavor compounds by biotechnological processes has a potential interest for the food industry. The use of natural available substrates and enzymes is an essential part of the process design, because the products may obtain natural label. In this study, direct esterification of citronellol and geraniol with short-chain fatty acids catalyzed by free lipase from Mucor miehei was performed with high yields in n-hexane. The effects of the acid:alcohol ratio on the bioconversion rate of increasing chain length esters was investigated. To reach the optimum yield, substrates and enzyme concentration were determined. The inhibiting effects of acid are strongly attenuated by reducing the quantity of acid and increasing the amount of enzyme in media following the optimum values. Improvements have been made to increase the ester purity. The consumption of excess substrate by adding calculated amounts of acid gives a 10% yield enhancement, and leads to 100% pure terpenyl esters. The first steps to a scale-up application were attempted using a reactor that allowed us to produce ester quantities up to 100 cm3. Separation and purification of the products were treated with success, underlining the lipase stability and efficiency under the conditions of this study. The ability to recover the enzyme, and reusing it in bioconversions, plays a major role in reducing the cost of the overall process.

Novel Enzyme Family Found in Filamentous Fungi Catalyzing trans-4-Hydroxylation of l-Pipecolic Acid

PubMed Central

Hibi, Makoto; Mori, Ryosuke; Miyake, Ryoma; Kawabata, Hiroshi; Kozono, Shoko; Takahashi, Satomi

2016-01-01

Hydroxypipecolic acids are bioactive compounds widely distributed in nature and are valuable building blocks for the organic synthesis of pharmaceuticals. We have found a novel hydroxylating enzyme with activity toward l-pipecolic acid (l-Pip) in a filamentous fungus, Fusarium oxysporum c8D. The enzyme l-Pip trans-4-hydroxylase (Pip4H) of F. oxysporum (FoPip4H) belongs to the Fe(II)/α-ketoglutarate-dependent dioxygenase superfamily, catalyzes the regio- and stereoselective hydroxylation of l-Pip, and produces optically pure trans-4-hydroxy-l-pipecolic acid (trans-4-l-HyPip). Amino acid sequence analysis revealed several fungal enzymes homologous with FoPip4H, and five of these also had l-Pip trans-4-hydroxylation activity. In particular, the homologous Pip4H enzyme derived from Aspergillus nidulans FGSC A4 (AnPip4H) had a broader substrate specificity spectrum than other homologues and reacted with the l and d forms of various cyclic and aliphatic amino acids. Using FoPip4H as a biocatalyst, a system for the preparative-scale production of chiral trans-4-l-HyPip was successfully developed. Thus, we report a fungal family of l-Pip hydroxylases and the enzymatic preparation of trans-4-l-HyPip, a bioactive compound and a constituent of secondary metabolites with useful physiological activities. PMID:26801577

Combinatorial structure of genome rearrangements scenarios.

PubMed

Ouangraoua, Aïda; Bergeron, Anne

2010-09-01

In genome rearrangement theory, one of the elusive questions raised in recent years is the enumeration of rearrangement scenarios between two genomes. This problem is related to the uniform generation of rearrangement scenarios and the derivation of tests of statistical significance of the properties of these scenarios. Here we give an exact formula for the number of double-cut-and-join (DCJ) rearrangement scenarios between two genomes. We also construct effective bijections between the set of scenarios that sort a component as well studied combinatorial objects such as parking functions, labeled trees, and prüfer codes.

Efficient production of fermentable sugars from oil palm empty fruit bunch by combined use of acid and whole cell culture-catalyzed hydrolyses.

PubMed

Li, Qingxin; Ng, Wei Ting; Puah, Sze Min; Bhaskar, Ravindran Vijay; Soh, Loon Siong; MacBeath, Calum; Parakattil, Pius; Green, Phil; Wu, Jin Chuan

2014-01-01

Empty fruit bunch (EFB) of oil palm trees was converted to fermentable sugars by the combined use of dilute acids and whole fungal cell culture-catalyzed hydrolyses. EFB (5%, w/v) was hydrolyzed in the presence of 0.5% H2 SO4 and 0.2% H3 PO4 at 160 °C for 10 Min. The solid fraction was separated from the acid hydrolysate by filtration and subjected to enzymatic hydrolysis at 50 °C using the whole cell culture of Trichoderma reesei RUT-C30 (2%, w/v), which was prepared by cultivation at 30 °C for 7 days to reach its maximal cellulase activity. The combined hydrolyses of EFB gave a total sugar yield of 82.0%. When used as carbon sources for cultivating Escherichia coli in M9 medium at 37 °C, the combined EFB hydrolysates were shown to be more favorable or at least as good as pure glucose for cell growth in terms of the higher (1.1 times) optical density of E. coli cells. The by-products generated during the acid-catalyzed hydrolysis did not seem to obviously affect cell growth. The combined use of acid and whole cell culture hydrolyses might be a commercially promising method for pretreatment of lignocellulose to get fermentable sugars. © 2013 International Union of Biochemistry and Molecular Biology, Inc.

Convenient synthesis of benzothiazoles and benzimidazoles through Brønsted acid catalyzed cyclization of 2-amino thiophenols/anilines with β-diketones.

PubMed

Mayo, Muhammad Shareef; Yu, Xiaoqiang; Zhou, Xiaoyu; Feng, Xiujuan; Yamamoto, Yoshinori; Bao, Ming

2014-02-07

Brønsted acid catalyzed cyclization reactions of 2-amino thiophenols/anilines with β-diketones under oxidant-, metal-, and radiation-free conditions are described. Various 2-substituted benzothiazoles/benzimidazoles are obtained in satisfactory to excellent yields. Different groups such as methyl, chloro, nitro, and methoxy linked on benzene rings were tolerated under the optimized reaction conditions.

Afrobatrachian mitochondrial genomes: genome reorganization, gene rearrangement mechanisms, and evolutionary trends of duplicated and rearranged genes

PubMed Central

2013-01-01

Background Mitochondrial genomic (mitogenomic) reorganizations are rarely found in closely-related animals, yet drastic reorganizations have been found in the Ranoides frogs. The phylogenetic relationships of the three major ranoid taxa (Natatanura, Microhylidae, and Afrobatrachia) have been problematic, and mitogenomic information for afrobatrachians has not been available. Several molecular models for mitochondrial (mt) gene rearrangements have been proposed, but observational evidence has been insufficient to evaluate them. Furthermore, evolutionary trends in rearranged mt genes have not been well understood. To gain molecular and phylogenetic insights into these issues, we analyzed the mt genomes of four afrobatrachian species (Breviceps adspersus, Hemisus marmoratus, Hyperolius marmoratus, and Trichobatrachus robustus) and performed molecular phylogenetic analyses. Furthermore we searched for two evolutionary patterns expected in the rearranged mt genes of ranoids. Results Extensively reorganized mt genomes having many duplicated and rearranged genes were found in three of the four afrobatrachians analyzed. In fact, Breviceps has the largest known mt genome among vertebrates. Although the kinds of duplicated and rearranged genes differed among these species, a remarkable gene rearrangement pattern of non-tandemly copied genes situated within tandemly-copied regions was commonly found. Furthermore, the existence of concerted evolution was observed between non-neighboring copies of triplicated 12S and 16S ribosomal RNA regions. Conclusions Phylogenetic analyses based on mitogenomic data support a close relationship between Afrobatrachia and Microhylidae, with their estimated divergence 100 million years ago consistent with present-day endemism of afrobatrachians on the African continent. The afrobatrachian mt data supported the first tandem and second non-tandem duplication model for mt gene rearrangements and the recombination-based model for concerted

N-Boc amines to oxazolidinones via Pd(II)/bis-sulfoxide/Brønsted acid co-catalyzed allylic C-H oxidation.

PubMed

Osberger, Thomas J; White, M Christina

2014-08-06

A Pd(II)/bis-sulfoxide/Brønsted acid catalyzed allylic C-H oxidation reaction for the synthesis of oxazolidinones from simple N-Boc amines is reported. A range of oxazolidinones are furnished in good yields (avg 63%) and excellent diastereoselectivities (avg 15:1) to furnish products regioisomeric from those previously obtained using allylic C-H amination reactions. Mechanistic studies suggest the role of the phosphoric acid is to furnish a Pd(II)bis-sulfoxide phosphate catalyst that promotes allylic C-H cleavage and π-allylPd functionalization with a weak, aprotic oxygen nucleophile and to assist in catalyst regeneration.

N-Boc Amines to Oxazolidinones via Pd(II)/Bis-sulfoxide/Brønsted Acid Co-Catalyzed Allylic C–H Oxidation

PubMed Central

2015-01-01

A Pd(II)/bis-sulfoxide/Brønsted acid catalyzed allylic C–H oxidation reaction for the synthesis of oxazolidinones from simple N-Boc amines is reported. A range of oxazolidinones are furnished in good yields (avg 63%) and excellent diastereoselectivities (avg 15:1) to furnish products regioisomeric from those previously obtained using allylic C–H amination reactions. Mechanistic studies suggest the role of the phosphoric acid is to furnish a Pd(II)bis-sulfoxide phosphate catalyst that promotes allylic C–H cleavage and π-allylPd functionalization with a weak, aprotic oxygen nucleophile and to assist in catalyst regeneration. PMID:24999765

Asymmetric Stetter reactions catalyzed by thiamine diphosphate-dependent enzymes.

PubMed

Kasparyan, Elena; Richter, Michael; Dresen, Carola; Walter, Lydia S; Fuchs, Georg; Leeper, Finian J; Wacker, Tobias; Andrade, Susana L A; Kolter, Geraldine; Pohl, Martina; Müller, Michael

2014-12-01

The intermolecular asymmetric Stetter reaction is an almost unexplored transformation for biocatalysts. Previously reported thiamine diphosphate (ThDP)-dependent PigD from Serratia marcescens is the first enzyme identified to catalyze the Stetter reaction of α,β-unsaturated ketones (Michael acceptor substrates) and α-keto acids. PigD is involved in the biosynthesis of the potent cytotoxic agent prodigiosin. Here, we describe the investigation of two new ThDP-dependent enzymes, SeAAS from Saccharopolyspora erythraea and HapD from Hahella chejuensis. Both show a high degree of homology to the amino acid sequence of PigD (39 and 51 %, respectively). The new enzymes were heterologously overproduced in Escherichia coli, and the yield of soluble protein was enhanced by co-expression of the chaperone genes groEL/ES. SeAAS and HapD catalyze intermolecular Stetter reactions in vitro with high enantioselectivity. The enzymes possess a characteristic substrate range with respect to Michael acceptor substrates. This provides support for a new type of ThDP-dependent enzymatic activity, which is abundant in various species and not restricted to prodigiosin biosynthesis in different strains. Moreover, PigD, SeAAS, and HapD are also able to catalyze asymmetric carbon-carbon bond formation reactions of aldehydes and α-keto acids, resulting in 2-hydroxy ketones.

Cytochrome P450 CYP716A254 catalyzes the formation of oleanolic acid from β-amyrin during oleanane-type triterpenoid saponins biosynthesis in Anemone flaccida.

PubMed

Zhan, Chuansong; Ahmed, Shakeel; Hu, Sheng; Dong, Shuang; Cai, Qian; Yang, Tewu; Wang, Xuekui; Li, Xiaohua; Hu, Xuebo

2018-01-01

Anemone flaccida Fr. Shmidt (Ranunculaceae), known as 'Di Wu' in China, is a perennial herb which has long been used to treat arthritis. The rhizome of A. flaccida contains pharmacologically active components i.e. oleanane-type triterpenoid saponins. Oleanolic acid is natural triterpenoid in plants with diverse biological activities. The biosynthesis of oleanolic acid involves cyclization of 2,3-oxidosqualene to the oleanane-type triterpenoid skeleton, followed by a series of oxidation reactions catalyzed by cytochrome P450 monooxygenase (CYP450). Previously, we identified four possible cytochrome P450 genes belonging to CYP716A subfamily from the transcriptome of A. flaccida. In this study, we identified one of those genes "CYP716A254" encoding a cytochrome P450 monooxygenase from A. flaccida that catalyzes the conversion of the β-amyrin into oleanolic acid. The heterologous expression of CYP716A254 in yeast resulted in oxidation of β-amyrin at the C-18 position to oleanolic acid production. These results provide an important basis for further studies of oleanane-type triterpenoid saponins synthesis in A. flaccida. Copyright © 2017 Elsevier Inc. All rights reserved.

Claisen thermally rearranged (CTR) polymers

PubMed Central

Tena, Alberto; Rangou, Sofia; Shishatskiy, Sergey; Filiz, Volkan; Abetz, Volker

2016-01-01

Thermally rearranged (TR) polymers, which are considered the next-generation of membrane materials because of their excellent transport properties and high thermal and chemical stability, are proven to have significant drawbacks because of the high temperature required for the rearrangement and low degree of conversion during this process. We demonstrate that using a [3,3]-sigmatropic rearrangement, the temperature required for the rearrangement of a solid glassy polymer was reduced by 200°C. Conversions of functionalized polyimide to polybenzoxazole of more than 97% were achieved. These highly mechanically stable polymers were almost five times more permeable and had more than two times higher degrees of conversion than the reference polymer treated under the same conditions. Properties of these second-generation TR polymers provide the possibility of preparing efficient polymer membranes in a form of, for example, thin-film composite membranes for various gas and liquid membrane separation applications. PMID:27482538

Claisen thermally rearranged (CTR) polymers.

PubMed

Tena, Alberto; Rangou, Sofia; Shishatskiy, Sergey; Filiz, Volkan; Abetz, Volker

2016-07-01

Thermally rearranged (TR) polymers, which are considered the next-generation of membrane materials because of their excellent transport properties and high thermal and chemical stability, are proven to have significant drawbacks because of the high temperature required for the rearrangement and low degree of conversion during this process. We demonstrate that using a [3,3]-sigmatropic rearrangement, the temperature required for the rearrangement of a solid glassy polymer was reduced by 200°C. Conversions of functionalized polyimide to polybenzoxazole of more than 97% were achieved. These highly mechanically stable polymers were almost five times more permeable and had more than two times higher degrees of conversion than the reference polymer treated under the same conditions. Properties of these second-generation TR polymers provide the possibility of preparing efficient polymer membranes in a form of, for example, thin-film composite membranes for various gas and liquid membrane separation applications.

Radical scavenging activity of lipophilized products from lipase-catalyzed transesterification of triolein with cinnamic and ferulic acids.

PubMed

Choo, Wee-Sim; Birch, Edward John

2009-02-01

Lipase-catalyzed transesterification of triolein with cinnamic and ferulic acids using an immobilized lipase from Candida antarctica (E.C. 3.1.1.3) was conducted to evaluate the antioxidant activity of the lipophilized products as model systems for enhanced protection of unsaturated oil. The lipophilized products were identified using ESI-MS. Free radical scavenging activity was determined using the DPPH radical method. The polarity of the solvents proved important in determining the radical scavenging activity of the substrates. Ferulic acid showed much higher radical scavenging activity than cinnamic acid, which has limited activity. The esterification of cinnamic acid and ferulic acid with triolein resulted in significant increase and decrease in the radical scavenging activity, respectively. These opposite effects were due to the effect of addition of electron-donating alkyl groups on the predominant mechanism of reaction (hydrogen atom transfer or electron transfer) of a species with DPPH. The effect of esterification of cinnamic acid was confirmed using ethyl cinnamate which greatly enhances the radical scavenging activity. Although, compared to the lipophilized cinnamic acid product, the activity was lower. The radical scavenging activity of the main component isolated from lipophilized cinnamic acid product using solid phase extraction, monocinnamoyl dioleoyl glycerol, was as good as the unseparated mixture of lipophilized product. Based on the ratio of a substrate to DPPH concentration, lipophilized ferulic acid was a much more efficient radical scavenger than lipophilized cinnamic acid.

Rearrangements of organic peroxides and related processes

PubMed Central

Yaremenko, Ivan A; Vil’, Vera A; Demchuk, Dmitry V

2016-01-01

Summary This review is the first to collate and summarize main data on named and unnamed rearrangement reactions of peroxides. It should be noted, that in the chemistry of peroxides two types of processes are considered under the term rearrangements. These are conventional rearrangements occurring with the retention of the molecular weight and transformations of one of the peroxide moieties after O–O-bond cleavage. Detailed information about the Baeyer−Villiger, Criegee, Hock, Kornblum−DeLaMare, Dakin, Elbs, Schenck, Smith, Wieland, and Story reactions is given. Unnamed rearrangements of organic peroxides and related processes are also analyzed. The rearrangements and related processes of important natural and synthetic peroxides are discussed separately. PMID:27559418

A novel on-line gold nanoparticle-catalyzed luminol chemiluminescence detector for high-performance liquid chromatography.

PubMed

Zhang, Qun Lin; Wu, Liang; Lv, Chen; Zhang, Xiao Yue

2012-06-15

A novel on-line gold nanoparticle-catalyzed luminol-H(2)O(2) chemiluminescence (CL) detector for high-performance liquid chromatography (HPLC) was established, in which gold nanoparticles were produced by the on-line reaction of H(2)O(2), NaHCO(3)-Na(2)CO(3) (buffer solution of luminol), and HAuCl(4). Eight phenolic compounds (gallic acid, protocatechuic acid, protocatechuic aldehyde, 2,5-dihydroxybenzoic acid, caffeic acid, 2,3-dihydroxybenzoic acid, (+)-catechin, and (-)-epicatechin) were chosen as the model compounds. Every separated phenolic compound in the column eluent strongly enhanced the CL signal of on-line gold nanoparticle-catalyzed luminol system. The CL and UV-visible absorption spectra and transmission electron microscopy studies were carried out, and the CL enhancement mechanism was ascribed to that the presence of phenolic compound promoted the on-line formation of 38-nm-diameter gold nanoparticles, which better catalyzed the luminol-H(2)O(2) CL reaction. The effects of methanol and phosphoric acid in the proposed HPLC configuration were performed by two gradient elution programs, and the baseline profile revealed that on-line gold nanoparticle-catalyzed luminol-H(2)O(2) CL detector had better compatibility than 38 nm gold colloids-luminol-H(2)O(2) CL detector. The proposed CL detector exhibits excellent analytical performance with the low detection limit (S/N=3) of 0.53-0.97 ng/mL (10.6-19.4 pg) phenolic compounds, and offers a new strategy for developing on-line nanoparticle-catalyzed CL detector for HPLC with sensitive analysis. Copyright © 2012 Elsevier B.V. All rights reserved.

Difference analysis of the enzymatic hydrolysis performance of acid-catalyzed steam-exploded corn stover before and after washing with water.

PubMed

Zhu, Junjun; Shi, Linli; Zhang, Lingling; Xu, Yong; Yong, Qiang; Ouyang, Jia; Yu, Shiyuan

2016-10-01

The difference in the enzymatic hydrolysis yield of acid-catalyzed steam-exploded corn stover (ASC) before and after washing with water reached approximately 15 % under the same conditions. The reasons for the difference in the yield between ASC and washed ASC (wASC) were determined through the analysis of the composition of ASC prehydrolyzate and sugar concentration of enzymatic hydrolyzate. Salts produced by neutralization (CaSO4, Na2SO4, K2SO4, and (NH4)2SO4), sugars (polysaccharides, oligosaccharides, and monosaccharides), sugar-degradation products (weak acids and furans), and lignin-degradation products (ethyl acetate extracts and nine main lignin-degradation products) were back-added to wASC. Results showed that these products, except furans, exerted negative effect on enzymatic hydrolysis. According to the characteristics of acid-catalyzed steam explosion pretreatment, the five sugar-degradation products' mixture and salts [Na2SO4, (NH4)2SO4] showed minimal negative inhibition effect on enzymatic hydrolysis. By contrast, furans demonstrated a promotion effect. Moreover, soluble sugars, such as 13 g/L xylose (decreased by 6.38 %), 5 g/L cellobiose (5.36 %), 10 g/L glucose (3.67 %), as well as lignin-degradation products, and ethyl acetate extracts (4.87 %), exhibited evident inhibition effect on enzymatic hydrolysis. Therefore, removal of soluble sugars and lignin-degradation products could effectively promote the enzymatic hydrolysis performance.

Diastereoselective Carbocyclization of 1,6-Heptadienes Triggered by Rhodium-Catalyzed Activation of an Olefinic C=H Bond**

PubMed Central

Aïssa, Christophe; Ho, Kelvin Y T; Tetlow, Daniel J; Pin-Nó, María

2014-01-01

The use of α,ω-dienes as functionalization reagents for olefinic carbon–hydrogen bonds has been rarely studied. Reported herein is the rhodium(I)-catalyzed rearrangement of prochiral 1,6-heptadienes into [2,2,1]-cycloheptane derivatives with concomitant creation of at least three stereogenic centers and complete diastereocontrol. Deuterium-labeling studies and the isolation of a key intermediate are consistent with a group-directed C=H bond activation, followed by two consecutive migratory insertions, with only the latter step being diastereoselective. PMID:24634225

Preparation of an amphiphilic resin-supported BINAP ligand and its use for rhodium-catalyzed asymmetric 1,4-addition of phenylboronic acid in water.

PubMed

Otomaru, Yusuke; Senda, Taichi; Hayashi, Tamio

2004-09-16

[reaction: see text] The axially chiral bisphosphine ligand, 2,2'-bis(diphenylphosphino)-1,1'-binaphthyl (binap), was supported on a polystyrene-poly(ethylene glycol) copolymer (PS-PEG) resin and was used successfully for the rhodium-catalyzed asymmetric 1,4-addition of phenylboronic acid to alpha,beta-unsaturated ketones in water.

Stereospecific Palladium-Catalyzed C-H Arylation of Pyroglutamic Acid Derivatives at the C3 Position Enabled by 8-Aminoquinoline as a Directing Group.

PubMed

Verho, Oscar; Maetani, Micah; Melillo, Bruno; Zoller, Jochen; Schreiber, Stuart L

2017-09-01

An efficient and stereospecific Pd-catalyzed protocol for the C-H arylation of pyroglutamic acid derivatives that uses 8-aminoquinoline as a directing group is described. The reaction was shown to proceed efficiently with a variety of aryl and heteroaryl iodides bearing different functional groups, giving C3-arylated cis products in good to high yields. Removal of the 8-aminoquinoline unit from these C-H arylation products enables access to synthetically useful cis and trans pyroglutamic acid-based building blocks.

Palladium-atom catalyzed formic acid decomposition and the switch of reaction mechanism with temperature.

PubMed

He, Nan; Li, Zhen Hua

2016-04-21

Formic acid decomposition (FAD) reaction has been an innovative way for hydrogen energy. Noble metal catalysts, especially palladium-containing nanoparticles, supported or unsupported, perform well in this reaction. Herein, we considered the simplest model, wherein one Pd atom is used as the FAD catalyst. With high-level theoretical calculations of CCSD(T)/CBS quality, we investigated all possible FAD pathways. The results show that FAD catalyzed by one Pd atom follows a different mechanism compared with that catalyzed by surfaces or larger clusters. At the initial stage of the reaction, FAD follows a dehydration route and is quickly poisoned by CO due to the formation of very stable PdCO. PdCO then becomes the actual catalyst for FAD at temperatures approximately below 1050 K. Beyond 1050 K, there is a switch of catalyst from PdCO to Pd atom. The results also show that dehydration is always favoured over dehydrogenation on either the Pd-atom or PdCO catalyst. On the Pd-atom catalyst, neither dehydrogenation nor dehydration follows the formate mechanism. In contrast, on the PdCO catalyst, dehydrogenation follows the formate mechanism, whereas dehydration does not. We also systematically investigated the performance of 24 density functional theory methods. We found that the performance of the double hybrid mPW2PLYP functional is the best, followed by the B3LYP, B3PW91, N12SX, M11, and B2PLYP functionals.

Protection of ascorbic acid from copper(II)-catalyzed oxidative degradation in the presence of flavonoids: quercetin, catechin and morin.

PubMed

Beker, Bilge Yildoğan; Sönmezoğlu, Inci; Imer, Filiz; Apak, Reşat

2011-08-01

Protection of ascorbic acid (AA) (vitamin C) from Cu(II)-catalyzed autoxidation is an important aspect of antioxidant chemistry. The autoxidation of AA in the absence and presence of Cu(II) ions was investigated in aerated solution at room temperature and I = 0.1 ionic strength (KNO(3)); the effects of three different flavonoids of similar structure (quercetin, morin and catechin) and their mixtures on the AA system were studied. The concentration of unoxidized AA remaining in solution was measured with the modified cupric ion reducing antioxidant capacity spectrophotometric method. The Cu(II)-catalyzed oxidation at pH 4.5 followed first-order kinetics with respect to AA concentration. Catalytic autoxidation of AA was inhibited to a greater extent by stable quercetin and morin complexes of Cu(II) than by catechin complex. The inhibitive effectiveness order of mixtures gives information about possible synergistic or antagonistic combinations of flavonoid antioxidants, which should be further confirmed with other antioxidant tests.

Synthesis of structured triacylglycerols containing caproic acid by lipase-catalyzed acidolysis: optimization by response surface methodology.

PubMed

Zhou, D; Xu, X; Mu, H; Høy, C E; Adler-Nissen, J

2001-12-01

Production in a batch reactor with a solvent-free system of structured triacylglycerols containing short-chain fatty acids by Lipozyme RM IM-catalyzed acidolysis between rapeseed oil and caproic acid was optimized using response surface methodology (RSM). Reaction time (t(r)), substrate ratio (S(r)), enzyme load (E(l), based on substrate), water content (W(c), based on enzyme), and reaction temperature (T(e)), the five most important parameters for the reaction, were chosen for the optimization. The range of each parameter was selected as follows: t(r) = 5-17 h; E(l) = 6-14 wt %; T(e) = 45-65 degrees C; S(r) = 2-6 mol/mol; and W(c) = 2-12 wt %. The biocatalyst was Lipozyme RM IM, in which Rhizomucor miehei lipase is immobilized on a resin. The incorporation of caproic acid into rapeseed oil was the main monitoring response. In addition, the contents of mono-incorporated structured triacylglycerols and di-incorporated structured triacylglycerols were also evaluated. The optimal reaction conditions for the incorporation of caproic acid and the content of di-incorporated structured triacylglycerols were as follows: t(r) = 17 h; S(r) = 5; E(l) = 14 wt %; W(c) = 10 wt %; T(e) = 65 degrees C. At these conditions, products with 55 mol % incorporation of caproic acid and 55 mol % di-incorporated structured triacylglycerols were obtained.

Improving fatty acid methyl ester production yield in a lipase-catalyzed process using waste frying oils as feedstock.

PubMed

Azócar, Laura; Ciudad, Gustavo; Heipieper, Hermann J; Muñoz, Robinson; Navia, Rodrigo

2010-06-01

The application of waste frying oil (WFO) mixed with rapeseed oil as a feedstock for the effective production of fatty acid methyl esters (FAME) in a lipase-catalyzed process was investigated. The response surface methodology (RSM) was used to optimize the interaction of four variables: the percentage of WFO in the mixed feedstock, the methanol-to-oil ratio, the dosage of Novozym 435 as a catalyst and the temperature. Furthermore, the addition of methanol to the reaction mixture in a second step after 8 h was shown to effectively diminish enzyme inhibition. Using this technique, the model predicted the optimal conditions that would reach 100% FAME, including a methanol-to-oil molar ratio of 3.8:1, 100% (wt) WFO, 15% (wt) Novozym 435 and incubation at 44.5 degrees C for 12 h with agitation at 200 rpm, and verification experiments confirmed the validity of the model. According to the model, the addition of WFO increased FAME production yield, which is largely due to its higher contents of monoacylglycerols, diacylglycerols and free fatty acids (in comparison to rapeseed oil), which are more available substrates for the enzymatic catalysis. Therefore, the replacement of rapeseed oil with WFO in Novozym 435-catalyzed processes could diminish biodiesel production costs since it is a less expensive feedstock that increases the production yield and could be a potential alternative for FAME production on an industrial scale. (c) 2009 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Detection of Nucleic Acids in Complex Samples via Magnetic Microbead-assisted Catalyzed Hairpin Assembly and "DD-A" FRET.

PubMed

Fang, Hongmei; Xie, Nuli; Ou, Min; Huang, Jin; Li, Wenshan; Wang, Qing; Liu, Jianbo; Yang, Xiaohai; Wang, Kemin

2018-05-21

Nucleic acids, as one kind of significant biomarkers, have attracted tremendous attention and exhibited immense value in fundamental studies and clinical applications. In this work, we developed a fluorescent assay for detecting nucleic acids in complex samples based on magnetic microbead (MMB)-assisted catalyzed hairpin assembly (CHA) and donor donor-acceptor fluorescence resonance energy transfer ("DD-A" FRET) signaling mechanism. Three types of DNA hairpin probes were employed in this system, including Capture, H1 (double FAM-labelled probe as FRET donor) and H2 (TAMRA-labelled probe as FRET acceptor). Firstly, the Captures immobilized on MMBs bound to targets in complex samples, and the sequences in Captures that could trigger catalyzed hairpin assembly (CHA) were exposed. Then, target-enriched MMBs complexes were separated and resuspended in the reaction buffer containing H1 and H2. As a result, numerous H1-H2 duplexes were formed during CHA process, inducing an obvious FRET signal. In contrast, CHA could not be trigger and the FRET signal was weak while target was absent. With the aid of magnetic separation and "DD-A" FRET, it was demonstrated to effectively eliminate errors from background interference. Importantly, this strategy realized amplified detection in buffer, with detection limits of microRNA as low as 34 pM. Furthermore, this method was successfully applied to detect microRNA-21 in serum and cell culture media. The results showed that our method has the potential for biomedical research and clinical application.

Influence of Pb 2+ ions in the H 2 oxidation on Pt catalyzed hydrogen diffusion anodes in sulfuric acid: presence of oscillatory phenomena

NASA Astrophysics Data System (ADS)

Expósito, E.; Sánchez-Sánchez, C. M.; Solla-Gullón, J.; Montiel, V.

The influence of Pb 2+ ions in sulfuric acid medium on the behavior of a platinum catalyzed hydrogen diffusion electrode (HDE) in a filter press reactor has been studied. A voltammetric study of the H 2 oxidation reaction on a polyoriented platinum electrode and a platinum rotating disk electrode (RDE) in presence of lead ions in solution has also been carried out. Potential oscillations were found in galvanostatic experiments of H 2 oxidation using a HDE catalyzed with platinum when Pb 2+ ions are present in solution. This oscillatory phenomenon was also observed when hydrogen oxidation was carried out in presence of Pb 2+ ions using a platinum RDE. The oscillatory behavior observed has been attributed to an adsorption-oxidation-desorption process of lead on the platinum surface. Due to the low solubility of Pb 2+ in sulfuric acid, at high values of coverage, lead is oxidised to insoluble lead sulfate that blocks the Pt surface. The coupling of the dissolution of lead sulfate and the Pb electrochemical adsorption-oxidation processes cause the oscillatory phenomenon.

Rhodium-catalyzed 1,4-addition of arylboronic acids to alpha,beta-unsaturated carbonyl compounds: large accelerating effects of bases and ligands.

PubMed

Itooka, Ryoh; Iguchi, Yuki; Miyaura, Norio

2003-07-25

The effects of ligands and bases in the rhodium(I)-catalyzed 1,4-addition of arylboronic acids to alpha,beta-unsaturated carbonyl compounds were reinvestigated to carry out the reaction under mild conditions. Rhodium(I) complexes possessing a 1,5-cyclooctadiene (cod) and a hydroxo ligand such as [RhOH(cod)](2) exhibited excellent catalyst activities compared to those of the corresponding rhodium-acac or -chloro complexes and their phosphine derivatives. The reaction was further accelerated in the presence of KOH, thus allowing the 1,4-addition even at 0 degrees C. A cationic rhodium(I)-(R)-binap complex, [Rh(R-binap)(nbd)]BF(4), catalyzed the reaction at 25-50 degrees C in the presence of Et(3)N with high enantioselectivities of up to 99% ee for alpha,beta-unsaturated ketones, 92% for aldehydes, 94% for esters, and 92% for amides.

Chromosome-specific staining to detect genetic rearrangements associated with chromosome 3 and/or chromosome 17

DOEpatents

Gray, Joe W.; Pinkel, Daniel; Kallioniemi, Olli-Pekka; Kallioniemi, Anne; Sakamoto, Masaru

2009-10-06

Methods and compositions for staining based upon nucleic acid sequence that employ nudeic nucleic acid probes are provided. Said methods produce staining patterns that can be tailored for specific cytogenetic analyses. Said probes are appropriate for in situ hybridization and stain both interphase and metaphase chromosomal material with reliable signals. The nucleic acid probes are typically of a complexity greater than 50 kb, the complexity depending upon the cytogenetic application. Methods and reagents are provided for the detection of genetic rearrangements. Probes and test kits are provided for use in detecting genetic rearrangements, particularly for use in tumor cytogenetics, in the detection of disease related loci, specifically cancer, such as chronic myelogenous leukemia (CML), retinoblastoma, ovarian and uterine cancers, and for biological dosimetry. Methods and reagents are described for cytogenetic research, for the differentiation of cytogenetically similar but genetically different diseases, and for many prognostic and diagnostic applications.

Analysis of genome rearrangement by block-interchanges.

PubMed

Lu, Chin Lung; Lin, Ying Chih; Huang, Yen Lin; Tang, Chuan Yi

2007-01-01

Block-interchanges are a new kind of genome rearrangements that affect the gene order in a chromosome by swapping two nonintersecting blocks of genes of any length. More recently, the study of such rearrangements is becoming increasingly important because of its applications in molecular evolution. Usually, this kind of study requires to solve a combinatorial problem, called the block-interchange distance problem, which is to find a minimum number of block-interchanges between two given gene orders of linear/circular chromosomes to transform one gene order into another. In this chapter, we shall introduce the basics of block-interchange rearrangements and permutation groups in algebra that are useful in analyses of genome rearrangements. In addition, we shall present a simple algorithm on the basis of permutation groups to efficiently solve the block-interchange distance problem, as well as ROBIN, a web server for the online analyses of block-interchange rearrangements.

A SABATH Methyltransferase from the moss Physcomitrella patens catalyzes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhao, Nan; Ferrer, Jean-Luc; Moon, Hong S

2012-01-01

Known SABATH methyltransferases, all of which were identified from seed plants, catalyze methylation of either the carboxyl group of a variety of low molecular weight metabolites or the nitrogen moiety of precursors of caffeine. In this study, the SABATH family from the bryophyte Physcomitrella patens was identified and characterized. Four SABATH-like sequences (PpSABATH1, PpSABATH2, PpSABATH3, and PpSABATH4) were identified from the P. patens genome. Only PpSABATH1 and PpSABATH2 showed expression in the leafy gametophyte of P. patens. Full-length cDNAs of PpSABATH1 and PpSABATH2 were cloned and expressed in soluble form in Escherichia coli. Recombinant PpSABATH1 and PpSABATH2 were tested formore » methyltransferase activity with a total of 75 compounds. While showing no activity with carboxylic acids or nitrogen-containing compounds, PpSABATH1 displayed methyltransferase activity with a number of thiols. PpSABATH2 did not show activity with any of the compounds tested. Among the thiols analyzed, PpSABATH1 showed the highest level of activity with thiobenzoic acid with an apparent Km value of 95.5 lM, which is comparable to those of known SABATHs. Using thiobenzoic acid as substrate, GC MS analysis indicated that the methylation catalyzed by PpSABATH1 is on the sulfur atom. The mechanism for S-methylation of thiols catalyzed by PpSABATH1 was partially revealed by homology-based structural modeling. The expression of PpSABATH1 was induced by the treatment of thiobenzoic acid. Further transgenic studies showed that tobacco plants overexpressing PpSABATH1 exhibited enhanced tolerance to thiobenzoic acid, suggesting that PpSABATH1 have a role in the detoxification of xenobiotic thiols.« less

Caffeine-catalyzed gels.

PubMed

DiCiccio, Angela M; Lee, Young-Ah Lucy; Glettig, Dean L; Walton, Elizabeth S E; de la Serna, Eva L; Montgomery, Veronica A; Grant, Tyler M; Langer, Robert; Traverso, Giovanni

2018-07-01

Covalently cross-linked gels are utilized in a broad range of biomedical applications though their synthesis often compromises easy implementation. Cross-linking reactions commonly utilize catalysts or conditions that can damage biologics and sensitive compounds, producing materials that require extensive post processing to achieve acceptable biocompatibility. As an alternative, we report a batch synthesis platform to produce covalently cross-linked materials appropriate for direct biomedical application enabled by green chemistry and commonly available food grade ingredients. Using caffeine, a mild base, to catalyze anhydrous carboxylate ring-opening of diglycidyl-ether functionalized monomers with citric acid as a tri-functional crosslinking agent we introduce a novel poly(ester-ether) gel synthesis platform. We demonstrate that biocompatible Caffeine Catalyzed Gels (CCGs) exhibit dynamic physical, chemical, and mechanical properties, which can be tailored in shape, surface texture, solvent response, cargo release, shear and tensile strength, among other potential attributes. The demonstrated versatility, low cost and facile synthesis of these CCGs renders them appropriate for a broad range of customized engineering applications including drug delivery constructs, tissue engineering scaffolds, and medical devices. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

19. SECOND FLOOR, CARDING MACHINE, BY 'CARDING SPECIALISTS, CO., LTD., ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

19. SECOND FLOOR, CARDING MACHINE, BY 'CARDING SPECIALISTS, CO., LTD., PELLON LAND WORKS, HALIFAX, ENGLAND, SN #M2983 14 (EST. DATE 1940'S+). - Bamberg Cotton Mill, Main Street, Bamberg, Bamberg County, SC

Compositions and methods for detecting gene rearrangements and translocations

DOEpatents

Rowley, Janet D.; Diaz, Manuel O.

2000-01-01

Disclosed is a series of nucleic acid probes for use in diagnosing and monitoring certain types of leukemia using, e.g., Southern and Northern blot analyses and fluorescence in situ hybridization (FISH). These probes detect rearrangements, such as translocations involving chromosome band 11q23 with other chromosomes bands, including 4q21, 6q27, 9p22, 19p13.3, in both dividing leukemic cells and interphase nuclei. The breakpoints in all such translocations are clustered within an 8.3 kb BamHI genomic region of the MLL gene. A novel 0.7 kb BamH1 cDNA fragment derived from this gene detects rearrangements on Southern blot analysis with a single BamHI restriction digest in all patients with the common 11q23 translocations and in patients with other 11q23 anomalies. Northern blot analyses are presented demonstrating that the MLL gene has multiple transcripts and that transcript size differentiates leukemic cells from normal cells. Also disclosed are MLL fusion proteins, MLL protein domains and anti-MLL antibodies.

20. SECOND FLOOR, CARDING MACHINE, BY 'CARDING SPECIALISTS, CO., LTD., ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

20. SECOND FLOOR, CARDING MACHINE, BY 'CARDING SPECIALISTS, CO., LTD., PELLON LAND WORKS, HALIFAX, ENGLAND, SN #M2983 14 (EST. DATE 1940'S+), OPPOSITE END - Bamberg Cotton Mill, Main Street, Bamberg, Bamberg County, SC

Structural rearrangements occurring upon cofactor binding in the Mycobacterium smegmatis β-ketoacyl-acyl carrier protein reductase MabA.

PubMed

Küssau, Tanja; Flipo, Marion; Van Wyk, Niel; Viljoen, Albertus; Olieric, Vincent; Kremer, Laurent; Blaise, Mickaël

2018-05-01

In mycobacteria, the ketoacyl-acyl carrier protein (ACP) reductase MabA (designated FabG in other bacteria) catalyzes the NADPH-dependent reduction of β-ketoacyl-ACP substrates to β-hydroxyacyl-ACP products. This first reductive step in the fatty-acid biosynthesis elongation cycle is essential for bacteria, which makes MabA/FabG an interesting drug target. To date, however, very few molecules targeting FabG have been discovered and MabA remains the only enzyme of the mycobacterial type II fatty-acid synthase that lacks specific inhibitors. Despite the existence of several MabA/FabG crystal structures, the structural rearrangement that occurs upon cofactor binding is still not fully understood. Therefore, unlocking this knowledge gap could help in the design of new inhibitors. Here, high-resolution crystal structures of MabA from Mycobacterium smegmatis in its apo, NADP + -bound and NADPH-bound forms are reported. Comparison of these crystal structures reveals the structural reorganization of the lid region covering the active site of the enzyme. The crystal structure of the apo form revealed numerous residues that trigger steric hindrance to the binding of NADPH and substrate. Upon NADPH binding, these residues are pushed away from the active site, allowing the enzyme to adopt an open conformation. The transition from an NADPH-bound to an NADP + -bound form is likely to facilitate release of the product. These results may be useful for subsequent rational drug design and/or for in silico drug-screening approaches targeting MabA/FabG.

Glycerol Dehydration to Acrolein Catalyzed by ZSM‐5 Zeolite in Supercritical Carbon Dioxide Medium

PubMed Central

Zou, Bin; Ren, Shoujie

2016-01-01

Abstract Supercritical carbon dioxide (SC‐CO2) has been used for the first time as a reaction medium for the dehydration of glycerol to acrolein catalyzed by a solid acid. Unprecedented catalyst stability over 528 hours of time‐on‐stream was achieved and the rate of coke deposition on the zeolite catalyst was the lowest among extensive previous studies, showing potential for industrial application. Coking pathways in SC‐CO2 were also elucidated for future development. The results have potential implications for other dehydration reactions catalyzed by solid acids. PMID:27796088

Phosphonate–Phosphinate Rearrangement

PubMed Central

2014-01-01

LiTMP metalated dimethyl N-Boc-phosphoramidates derived from 1-phenylethylamine and 1,2,3,4-tetrahydronaphthalen-1-ylamine highly selectively at the CH3O group to generate short-lived oxymethyllithiums. These isomerized to diastereomeric hydroxymethylphosphonamidates (phosphate–phosphonate rearrangement). However, s-BuLi converted the dimethyl N-Boc-phosphoramidate derived from 1-phenylethylamine to the N-Boc α-aminophosphonate preferentially. Only s-BuLi deprotonated dimethyl hydroxymethylphosphonamidates at the benzylic position and dimethyl N-Boc α-aminophosphonates at the CH3O group to induce phosphonate–phosphinate rearrangements. In the former case, the migration of the phosphorus substituent from the nitrogen to the carbon atom followed a retentive course with some racemization because of the involvement of a benzyllithium as an intermediate. PMID:25525945

Dehydrogenation, disproportionation and transfer hydrogenation reactions of formic acid catalyzed by molybdenum hydride compounds.

PubMed

Neary, Michelle C; Parkin, Gerard

2015-03-01

The cyclopentadienyl molybdenum hydride compounds, Cp R Mo(PMe 3 ) 3- x (CO) x H (Cp R = Cp, Cp*; x = 0, 1, 2 or 3), are catalysts for the dehydrogenation of formic acid, with the most active catalysts having the composition Cp R Mo(PMe 3 ) 2 (CO)H. The mechanism of the catalytic cycle is proposed to involve (i) protonation of the molybdenum hydride complex, (ii) elimination of H 2 and coordination of formate, and (iii) decarboxylation of the formate ligand to regenerate the hydride species. NMR spectroscopy indicates that the nature of the resting state depends on the composition of the catalyst. For example, (i) the resting states for the CpMo(CO) 3 H and CpMo(PMe 3 )(CO) 2 H systems are the hydride complexes themselves, (ii) the resting state for the CpMo(PMe 3 ) 3 H system is the protonated species [CpMo(PMe 3 ) 3 H 2 ] + , and (iii) the resting state for the CpMo(PMe 3 ) 2 (CO)H system is the formate complex, CpMo(PMe 3 ) 2 (CO)(κ 1 -O 2 CH), in the presence of a high concentration of formic acid, but CpMo(PMe 3 ) 2 (CO)H when the concentration of acid is low. While CO 2 and H 2 are the principal products of the catalytic reaction induced by Cp R Mo(PMe 3 ) 3- x (CO) x H, methanol and methyl formate are also observed. The generation of methanol is a consequence of disproportionation of formic acid, while methyl formate is a product of subsequent esterification. The disproportionation of formic acid is a manifestation of a transfer hydrogenation reaction, which may also be applied to the reduction of aldehydes and ketones. Thus, CpMo(CO) 3 H also catalyzes the reduction of a variety of ketones and aldehydes to alcohols by formic acid, via a mechanism that involves ionic hydrogenation.

Recurrent DNA inversion rearrangements in the human genome

PubMed Central

Flores, Margarita; Morales, Lucía; Gonzaga-Jauregui, Claudia; Domínguez-Vidaña, Rocío; Zepeda, Cinthya; Yañez, Omar; Gutiérrez, María; Lemus, Tzitziki; Valle, David; Avila, Ma. Carmen; Blanco, Daniel; Medina-Ruiz, Sofía; Meza, Karla; Ayala, Erandi; García, Delfino; Bustos, Patricia; González, Víctor; Girard, Lourdes; Tusie-Luna, Teresa; Dávila, Guillermo; Palacios, Rafael

2007-01-01

Several lines of evidence suggest that reiterated sequences in the human genome are targets for nonallelic homologous recombination (NAHR), which facilitates genomic rearrangements. We have used a PCR-based approach to identify breakpoint regions of rearranged structures in the human genome. In particular, we have identified intrachromosomal identical repeats that are located in reverse orientation, which may lead to chromosomal inversions. A bioinformatic workflow pathway to select appropriate regions for analysis was developed. Three such regions overlapping with known human genes, located on chromosomes 3, 15, and 19, were analyzed. The relative proportion of wild-type to rearranged structures was determined in DNA samples from blood obtained from different, unrelated individuals. The results obtained indicate that recurrent genomic rearrangements occur at relatively high frequency in somatic cells. Interestingly, the rearrangements studied were significantly more abundant in adults than in newborn individuals, suggesting that such DNA rearrangements might start to appear during embryogenesis or fetal life and continue to accumulate after birth. The relevance of our results in regard to human genomic variation is discussed. PMID:17389356

Membrane protein complexes catalyze both 4- and 3-hydroxylation of cinnamic acid derivatives in monolignol biosynthesis

PubMed Central

Chen, Hsi-Chuan; Li, Quanzi; Shuford, Christopher M.; Liu, Jie; Muddiman, David C.; Sederoff, Ronald R.; Chiang, Vincent L.

2011-01-01

The hydroxylation of 4- and 3-ring carbons of cinnamic acid derivatives during monolignol biosynthesis are key steps that determine the structure and properties of lignin. Individual enzymes have been thought to catalyze these reactions. In stem differentiating xylem (SDX) of Populus trichocarpa, two cinnamic acid 4-hydroxylases (PtrC4H1 and PtrC4H2) and a p-coumaroyl ester 3-hydroxylase (PtrC3H3) are the enzymes involved in these reactions. Here we present evidence that these hydroxylases interact, forming heterodimeric (PtrC4H1/C4H2, PtrC4H1/C3H3, and PtrC4H2/C3H3) and heterotrimeric (PtrC4H1/C4H2/C3H3) membrane protein complexes. Enzyme kinetics using yeast recombinant proteins demonstrated that the enzymatic efficiency (Vmax/km) for any of the complexes is 70–6,500 times greater than that of the individual proteins. The highest increase in efficiency was found for the PtrC4H1/C4H2/C3H3-mediated p-coumaroyl ester 3-hydroxylation. Affinity purification-quantitative mass spectrometry, bimolecular fluorescence complementation, chemical cross-linking, and reciprocal coimmunoprecipitation provide further evidence for these multiprotein complexes. The activities of the recombinant and SDX plant proteins demonstrate two protein-complex–mediated 3-hydroxylation paths in monolignol biosynthesis in P. trichocarpa SDX; one converts p-coumaric acid to caffeic acid and the other converts p-coumaroyl shikimic acid to caffeoyl shikimic acid. Cinnamic acid 4-hydroxylation is also mediated by the same protein complexes. These results provide direct evidence for functional involvement of membrane protein complexes in monolignol biosynthesis. PMID:22160716

Omega-3 fatty acids modulate Weibel-Palade body degranulation and actin cytoskeleton rearrangement in PMA-stimulated human umbilical vein endothelial cells.

PubMed

Bürgin-Maunder, Corinna S; Brooks, Peter R; Russell, Fraser D

2013-11-08

Long chain omega-3 polyunsaturated fatty acids (LC n-3 PUFAs) produce cardiovascular benefits by improving endothelial function. Endothelial cells store von Willebrand factor (vWF) in cytoplasmic Weibel-Palade bodies (WPBs). We examined whether LC n-3 PUFAs regulate WPB degranulation using cultured human umbilical vein endothelial cells (HUVECs). HUVECs were incubated with or without 75 or 120 µM docosahexaenoic acid or eicosapentaenoic acid for 5 days at 37 °C. WPB degranulation was stimulated using phorbol 12-myristate 13-acetate (PMA), and this was assessed by immunocytochemical staining for vWF. Actin reorganization was determined using phalloidin-TRITC staining. We found that PMA stimulated WPB degranulation, and that this was significantly reduced by prior incubation of cells with LC n-3 PUFAs. In these cells, WPBs had rounded rather than rod-shaped morphology and localized to the perinuclear region, suggesting interference with cytoskeletal remodeling that is necessary for complete WPB degranulation. In line with this, actin rearrangement was altered in cells containing perinuclear WPBs, where cells exhibited a thickened actin rim in the absence of prominent cytoplasmic stress fibers. These findings indicate that LC n-3 PUFAs provide some protection against WBP degranulation, and may contribute to an improved understanding of the anti-thrombotic effects previously attributed to LC n-3 PUFAs.

Novel Dextranase Catalyzing Cycloisomaltooligosaccharide Formation and Identification of Catalytic Amino Acids and Their Functions Using Chemical Rescue Approach*

PubMed Central

Kim, Young-Min; Kiso, Yoshiaki; Muraki, Tomoe; Kang, Min-Sun; Nakai, Hiroyuki; Saburi, Wataru; Lang, Weeranuch; Kang, Hee-Kwon; Okuyama, Masayuki; Mori, Haruhide; Suzuki, Ryuichiro; Funane, Kazumi; Suzuki, Nobuhiro; Momma, Mitsuru; Fujimoto, Zui; Oguma, Tetsuya; Kobayashi, Mikihiko; Kim, Doman; Kimura, Atsuo

2012-01-01

A novel endodextranase from Paenibacillus sp. (Paenibacillus sp. dextranase; PsDex) was found to mainly produce isomaltotetraose and small amounts of cycloisomaltooligosaccharides (CIs) with a degree of polymerization of 7–14 from dextran. The 1,696-amino acid sequence belonging to the glycosyl hydrolase family 66 (GH-66) has a long insertion (632 residues; Thr451–Val1082), a portion of which shares identity (35% at Ala39–Ser1304 of PsDex) with Pro32–Ala755 of CI glucanotransferase (CITase), a GH-66 enzyme that catalyzes the formation of CIs from dextran. This homologous sequence (Val837–Met932 for PsDex and Tyr404–Tyr492 for CITase), similar to carbohydrate-binding module 35, was not found in other endodextranases (Dexs) devoid of CITase activity. These results support the classification of GH-66 enzymes into three types: (i) Dex showing only dextranolytic activity, (ii) Dex catalyzing hydrolysis with low cyclization activity, and (iii) CITase showing CI-forming activity with low dextranolytic activity. The fact that a C-terminal truncated enzyme (having Ala39–Ser1304) has 50% wild-type PsDex activity indicates that the C-terminal 392 residues are not involved in hydrolysis. GH-66 enzymes possess four conserved acidic residues (Asp189, Asp340, Glu412, and Asp1254 of PsDex) of catalytic candidates. Their amide mutants decreased activity (11,500 to 140,000 times), and D1254N had 36% activity. A chemical rescue approach was applied to D189A, D340G, and E412Q using α-isomaltotetraosyl fluoride with NaN3. D340G or E412Q formed a β- or α-isomaltotetraosyl azide, respectively, strongly indicating Asp340 and Glu412 as a nucleophile and acid/base catalyst, respectively. Interestingly, D189A synthesized small sized dextran from α-isomaltotetraosyl fluoride in the presence of NaN3. PMID:22461618

Biotransformation and Rearrangement of Laromustine.

PubMed

Nassar, Alaa-Eldin F; Wisnewski, Adam V; King, Ivan

2016-08-01

This review highlights the recent research into the biotransformations and rearrangement of the sulfonylhydrazine-alkylating agent laromustine. Incubation of [(14)C]laromustine with rat, dog, monkey, and human liver microsomes produced eight radioactive components (C-1 to C-8). There was little difference in the metabolite profile among the species examined, partly because NADPH was not required for the formation of most components, which instead involved decomposition and/or hydrolysis. The exception was C-7, a hydroxylated metabolite, largely formed by CYP2B6 and CYP3A4/5. Liquid chromatography-multistage mass spectrometry (LC-MS(n)) studies determined that collision-induced dissociation, and not biotransformation or enzyme catalysis, produced the unique mass spectral rearrangement. Accurate mass measurements performed with a Fourier-transform ion cyclotron resonance mass spectrometer (FTICR-MS) significantly aided determination of the elemental compositions of the fragments and in the case of laromustine revealed the possibility of rearrangement. Further, collision-induced dissociation produced the loss of nitrogen (N2) and methylsulfonyl and methyl isocyanate moieties. The rearrangement, metabolite/decomposition products, and conjugation reactions were analyzed utilizing hydrogen-deuterium exchange, exact mass, (13)C-labeled laromustine, nuclear magnetic resonance spectroscopy (NMR), and LC-MS(n) experiments to assist with the assignments of these fragments and possible mechanistic rearrangement. Such techniques produced valuable insights into these functions: 1) Cytochrome P450 is involved in C-7 formation but plays little or no role in the conversion of [(14)C]laromustine to C-1 through C-6 and C-8; 2) the relative abundance of individual degradation/metabolite products was not species-dependent; and 3) laromustine produces several reactive intermediates that may produce the toxicities seen in the clinical trials. Copyright © 2016 by The American Society for

Theoretical study on the mechanism of aqueous synthesis of formic acid catalyzed by [Ru3+]-EDTA complex.

PubMed

Chen, Zhe-Ning; Chan, Kwong-Yu; Pulleri, Jayasree K; Kong, Jing; Hu, Hao

2015-02-16

Because formic acid can be effectively decomposed by catalysis into very pure hydrogen gas, the synthesis of formic acid, especially using CO and H2O as an intermediate of the water gas shift reaction (WGSR), bears important application significance in industrial hydrogen gas production. Here we report a theoretical study on the mechanism of efficient preparation of formic acid using CO and H2O catalyzed by a water-soluble [Ru(3+)]-EDTA complex. To determine the feasibility of using the [Ru(3+)]-EDTA catalyst to produce CO-free hydrogen gas in WGSR, two probable reaction paths have been examined: one synthesizes formic acid, while the other converts the reactants directly into CO2 and H2, the final products of WGSR. Our calculation results provide a detailed mechanistic rationalization for the experimentally observed selective synthesis of HCOOH by the [Ru(3+)]-EDTA catalyst. The results support the applicability of using the [Ru(3+)]-EDTA catalyst to efficiently synthesize formic acid for hydrogen production. Careful analyses of the electronic structure and interactions of different reaction complexes suggest that the selectivity of the reaction processes is achieved through the proper charge/valence state of the metal center of the [Ru(3+)]-EDTA complex. With the catalytic roles of the ruthenium center and the EDTA ligand being carefully understood, the detailed mechanistic information obtained in this study will help to design more efficient catalysts for the preparation of formic acid and further to produce CO-free H2 at ambient temperature.

Acid-catalyzed condensed-phase reactions of limonene and terpineol and their impacts on gas-to-particle partitioning in the formation of organic aerosols.

PubMed

Li, Yong Jie; Cheong, Gema Y L; Lau, Arthur P S; Chan, Chak K

2010-07-15

We investigated the condensed-phase reactions of biogenic VOCs with C double bond C bonds (limonene, C(10)H(16), and terpineol, C(10)H(18)O) catalyzed by sulfuric acid by both bulk solution (BS) experiments and gas-particle (GP) experiments using a flow cell reactor. Product analysis by gas chromatography-mass spectrometry (GC-MS) showed that cationic polymerization led to dimeric and trimeric product formation under conditions of relative humidity (RH) <20% (in the GP experiments) and a sulfuric acid concentration of 57.8 wt % (in the BS experiments), while hydration occurred under conditions of RH > 20% (in the GP experiments) and sulfuric acid concentrations of 46.3 wt % or lower (in the BS experiments). Apparent partitioning coefficients (K(p,rxn)) were estimated from the GP experiments by including the reaction products. Only under extremely low RH conditions (RH < 5%) did the values of K(p,rxn) ( approximately 5 x 10(-6) m(3)/microg for limonene and approximately 2 x 10(-5) m(3)/microg for terpineol) substantially exceed the physical partitioning coefficients (K(p) = 6.5 x 10(-8) m(3)/microg for limonene and =2.3 x 10(-6) m(3)/microg for terpineol) derived from the absorptive partitioning theory. At RH higher than 5%, the apparent partitioning coefficients (K(p,rxn)) of both limonene and terpineol were in the same order of magnitude as the K(p) values derived from the absorptive partitioning theory. Compared with other conditions including VOC concentration and degree of neutralization (by ammonium) of acidic particles, RH is a critical parameter that influences both the reaction mechanisms and the uptake ability (K(p,rxn) values) of these processes. The finding suggests that RH needs to be considered when taking the effects of acid-catalyzed reactions into account in estimating organic aerosol formation from C double bond C containing VOCs.

Glycerol Dehydration to Acrolein Catalyzed by ZSM-5 Zeolite in Supercritical Carbon Dioxide Medium.

PubMed

Zou, Bin; Ren, Shoujie; Ye, X Philip

2016-12-08

Supercritical carbon dioxide (SC-CO 2 ) has been used for the first time as a reaction medium for the dehydration of glycerol to acrolein catalyzed by a solid acid. Unprecedented catalyst stability over 528 hours of time-on-stream was achieved and the rate of coke deposition on the zeolite catalyst was the lowest among extensive previous studies, showing potential for industrial application. Coking pathways in SC-CO 2 were also elucidated for future development. The results have potential implications for other dehydration reactions catalyzed by solid acids. © 2016 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Expedient synthesis of fused azepine derivatives using a sequential rhodium(II)-catalyzed cyclopropanation/1-aza-Cope rearrangement of dienyltriazoles.

PubMed

Schultz, Erica E; Lindsay, Vincent N G; Sarpong, Richmond

2014-09-08

A general method for the formation of fused dihydroazepine derivatives from 1-sulfonyl-1,2,3-triazoles bearing a tethered diene is reported. The process involves an intramolecular cyclopropanation of an α-imino rhodium(II) carbenoid, leading to a transient 1-imino-2-vinylcyclopropane intermediate which rapidly undergoes a 1-aza-Cope rearrangement to generate fused dihydroazepine derivatives in moderate to excellent yields. The reaction proceeds with similar efficiency on gram scale. The use of catalyst-free conditions leads to the formation of a novel [4.4.0] bicyclic heterocycle. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Aromatic aldehyde-catalyzed gas-phase decarboxylation of amino acid anion via imine intermediate: An experimental and theoretical study

NASA Astrophysics Data System (ADS)

Xiang, Zhang

2013-10-01

It is generally appreciated that carbonyl compound can promote the decarboxylation of the amino acid. In this paper, we have performed the experimental and theoretical investigation into the gas-phase decarboxylation of the amino acid anion catalyzed by the aromatic aldehyde via the imine intermediate on the basis of the tandem mass spectrometry (MS/MS) technique and density functional theory (DFT) calculation. The results show that the aromatic aldehyde can achieve a remarkable catalytic effect. Moreover, the catalytic mechanism varies according to the type of amino acid: (i) The decarboxylation of α-amino acid anion is determined by the direct dissociation of the Csbnd C bond adjacent to the carboxylate, for the resulting carbanion can be well stabilized by the conjugation between α-carbon, Cdbnd N bond and benzene ring. (ii) The decarboxylation of non-α-amino acid anion proceeds via a SN2-like transition state, in which the dissociation of the Csbnd C bond adjacent to the carboxylate and attacking of the resulting carbanion to the Cdbnd N bond or benzene ring take place at the same time. Specifically, for β-alanine, the resulting carbanion preferentially attacks the benzene ring leading to the benzene anion, because attacking the Cdbnd N bond in the decarboxylation can produce the unstable three or four-membered ring anion. For the other non-α-amino acid anion, the Cdbnd N bond preferentially participates in the decarboxylation, which leads to the pediocratic nitrogen anion.

An Au(I)-catalyzed rearrangement/cyclization cascade toward the synthesis of 2-substituted-1,4,5,6-tetrahydrocyclopenta[b]pyrrole.

PubMed

Mou, Xue-Qing; Xu, Zheng-Liang; Wang, Shao-Hua; Zhu, Dao-Yong; Wang, Jie; Bao, Wen; Zhou, Shi-Jiang; Yang, Chao; Zhang, Di

2015-08-04

An Au(I)-catalyzed tandem reaction for the synthesis of 2-phenyl-1,4,5,6-tetrahydrocyclopenta[b]pyrrole derivatives from 1-(1-hydroxy-3-phenylprop-2-yn-1-yl)cyclobutanol and primary amines or NH4OAc has been developed to afford a series of polysubstituted pyrroles in moderate to good yields.

Chromosome Rearrangements Recovered following Transformation of Neurospora Crassa

PubMed Central

Perkins, D. D.; Kinsey, J. A.; Asch, D. K.; Frederick, G. D.

1993-01-01

New chromosome rearrangements were found in 10% or more of mitotically stable transformants. This was shown for transformations involving a variety of different markers, vectors and recipient strains. Breakpoints were randomly distributed among the seven linkage groups. Controls using untransformed protoplasts of the same strains contained almost no rearrangements. A study of molecularly characterized Am(+) transformants showed that rearrangements are frequent when multiple ectopic integration events have occurred. In contrast, rearrangements are absent or infrequent when only the resident locus is restored to am(+) by a homologous event. Sequences of the transforming vector were genetically linked to breakpoints in 6 of 10 translocations that were examined using Southern hybridization or colony blots. PMID:8349106

Sorting permutations by prefix and suffix rearrangements.

PubMed

Lintzmayer, Carla Negri; Fertin, Guillaume; Dias, Zanoni

2017-02-01

Some interesting combinatorial problems have been motivated by genome rearrangements, which are mutations that affect large portions of a genome. When we represent genomes as permutations, the goal is to transform a given permutation into the identity permutation with the minimum number of rearrangements. When they affect segments from the beginning (respectively end) of the permutation, they are called prefix (respectively suffix) rearrangements. This paper presents results for rearrangement problems that involve prefix and suffix versions of reversals and transpositions considering unsigned and signed permutations. We give 2-approximation and ([Formula: see text])-approximation algorithms for these problems, where [Formula: see text] is a constant divided by the number of breakpoints (pairs of consecutive elements that should not be consecutive in the identity permutation) in the input permutation. We also give bounds for the diameters concerning these problems and provide ways of improving the practical results of our algorithms.

Access to Different Isomeric Dibenzoxazepinones through Copper-Catalyzed C-H Etherification and C-N Bond Construction with Controllable Smiles Rearrangement.

PubMed

Zhou, Yunfei; Zhu, Jianming; Li, Bo; Zhang, Yong; Feng, Jia; Hall, Adrian; Shi, Jiye; Zhu, Weiliang

2016-02-05

An efficient new way to access two regio-isomeric dibenzoxazepinones is reported from 8-aminoquinoline benzamides and 2-bromophenols. Through choice of conditions, the reaction proceeds either through a sequential C-H etherification and subsequent Goldberg reaction, both controlled by the aminoquinoline group and Cu(I), or via a C-H etherification and subsequent Smiles rearrangement promoted by Cu(II) and t-BuOK. The 8-aminoquinoline moiety, e.g., 8-amino-5-methoxyquinoline, is readily removable from the structures of dibenzoxazepinones under moderate conditions.

Impact of Zeolite Aging in Hot Liquid Water on Activity for Acid-Catalyzed Dehydration of Alcohols.

PubMed

Vjunov, Aleksei; Derewinski, Miroslaw A; Fulton, John L; Camaioni, Donald M; Lercher, Johannes A

2015-08-19

The location and stability of Brønsted acid sites catalytically active in zeolites during aqueous phase dehydration of alcohols were studied on the example of cyclohexanol. The catalytically active hydronium ions originate from Brønsted acid sites (BAS) of the zeolite that are formed by framework tetrahedral Si atom substitution by Al. Al K-edge extended X-ray absorption fine structure (EXAFS) and (27)Al magic angle spinning (MAS) nuclear magnetic resonance (NMR) spectroscopies in combination with density functional theory (DFT) calculations are used to determine the distribution of tetrahedral Al sites (Al T-sites) both qualitatively and quantitatively for both parent and HBEA catalysts aged in water prior to catalytic testing. The aging procedure leads to partial degradation of the zeolite framework evidenced from the decrease of material crystallinity (XRD) as well as sorption capacity (BET). With the exception of one commercial zeolite sample, which had the highest concentration of framework silanol-defects, there is no evidence of Al coordination modification after aging in water. The catalyst weight-normalized dehydration rate correlated best with the sum of strong and weak Brønsted acidic protons both able to generate the hydrated hydronium ions. All hydronium ions were equally active for the acid-catalyzed reactions in water. Zeolite aging in hot water prior to catalysis decreased the weight normalized dehydration reaction rate compared to that of the parent HBEA, which is attributed to the reduced concentration of accessible Brønsted acid sites. Sites are hypothesized to be blocked due to reprecipitation of silica dissolved during framework hydrolysis in the aging procedure.

The Chirped-Pulse Fourier Transform Microwave Cp-Ftmw Spectrum and Potential Energy Calculations for AN Aromatic Claisen Rearrangement Molecule, Allyl Phenyl Ether

NASA Astrophysics Data System (ADS)

Grubbs, G. S. Grubbs, Ii; Cooke, S. A.; Novick, Stewart E.

2012-06-01

Claisen rearrangement ethers are a fundamental organic, pericyclic rearrangement reaction reagent. In the mechanism of a Claisen rearrangement, a vinyl allyl ether is needed to provide the necessary Lewis acid/base sites on the molecule for the rearrangement and are simply heated. This rearrangement was first discovered by heating up the title molecule, allyl phenyl ether. However, much like the Diels-Alder, Cope, and other pericyclic reactions, conformation and coordination of chemical groups is key to the Claisen mechanism. In this study, the authors present some structural characteristics of allyl phenyl ether from an analysis of the microwave spectra in the 8-14 GHz region using a CP-FTMW spectrometer. This is, to the authors knowledge, the first known microwave region study of the title molecule. Three conformers have been observed and assigned to date and will be discussed. Along with the rotational spectra, geometry calculations and potential energy surfaces performed at the MP2/6-311G++(3d,2p) level will be discussed and compared to the experimental results. Modeling the Claisen aromatic rearrangement mechanism using CP-FTMW spectroscopy will also be discussed. L. Claisen Chemische Berichte 45, 3157, October 1912.

PhdA Catalyzes the First Step of Phenazine-1-Carboxylic Acid Degradation in Mycobacterium fortuitum.

PubMed

Costa, Kyle C; Moskatel, Leon S; Meirelles, Lucas A; Newman, Dianne K

2018-05-15

Phenazines are a class of bacterially produced redox-active metabolites that are found in natural, industrial, and clinical environments. In Pseudomonas spp., phenazine-1-carboxylic acid (PCA)-the precursor of all phenazine metabolites-facilitates nutrient acquisition, biofilm formation, and competition with other organisms. While the removal of phenazines negatively impacts these activities, little is known about the genes or enzymes responsible for phenazine degradation by other organisms. Here, we report that the first step of PCA degradation by Mycobacterium fortuitum is catalyzed by a ph enazine- d egrading decarboxylase (PhdA). PhdA is related to members of the UbiD protein family that rely on a prenylated flavin mononucleotide cofactor for activity. The gene for PhdB, the enzyme responsible for cofactor synthesis, is present in a putative operon with the gene encoding PhdA in a region of the M. fortuitum genome that is essential for PCA degradation. PhdA and PhdB are present in all known PCA-degrading organisms from the Actinobacteria M. fortuitum can also catabolize other Pseudomonas -derived phenazines such as phenazine-1-carboxamide, 1-hydroxyphenazine, and pyocyanin. On the basis of our previous work and the current characterization of PhdA, we propose that degradation converges on a common intermediate: dihydroxyphenazine. An understanding of the genes responsible for degradation will enable targeted studies of phenazine degraders in diverse environments. IMPORTANCE Bacteria from phylogenetically diverse groups secrete redox-active metabolites that provide a fitness advantage for their producers. For example, phenazines from Pseudomonas spp. benefit the producers by facilitating anoxic survival and biofilm formation and additionally inhibit competitors by serving as antimicrobials. Phenazine-producing pseudomonads act as biocontrol agents by leveraging these antibiotic properties to inhibit plant pests. Despite this importance, the fate of phenazines in

Kinetics of non-catalyzed hydrolysis of tannin in high temperature liquid water*

PubMed Central

Lu, Li-li; Lu, Xiu-yang; Ma, Nan

2008-01-01

High temperature liquid water (HTLW) has drawn increasing attention as an environmentally benign medium for organic chemical reactions, especially acid-/base-catalyzed reactions. Non-catalyzed hydrolyses of gallotannin and tara tannin in HTLW for the simultaneous preparation of gallic acid (GA) and pyrogallol (PY) are under investigation in our laboratory. In this study, the hydrolysis kinetics of gallotannin and tara tannin were determined. The reaction is indicated to be a typical consecutive first-order one in which GA has formed as a main intermediate and PY as the final product. Selective decomposition of tannin in HTLW was proved to be possible by adjusting reaction temperature and time. The present results provide an important basic data and reference for the green preparation of GA and PY. PMID:18500780

Enantiomerically pure 3-aryl- and 3-hetaryl-2-hydroxypropanoic acids by chemoenzymatic reduction of 2-oxo acids.

PubMed

Sivanathan, Sivatharushan; Körber, Florian; Tent, Jannis Aron; Werner, Svenja; Scherkenbeck, Jürgen

2015-03-06

Phenyllactic acids are found in numerous natural products as well as in active substances used in medicine or plant protection. Enantiomerically pure phenyllactic acids are available by transition-metal-catalyzed hydrogenations or chemoenzymatic reductions of the corresponding 3-aryl-2-oxopropanoic acids. We show here that d-lactate dehydrogenase from Staphylococcus epidermidis reduces a broad spectrum of 2-oxo acids, which are difficult substrates for transition-metal-catalyzed reactions, with excellent enantioselectivities in a simple experimental setup.

[Inhibiting properties of stable nitroxyl radicals in reactions of linoleic acid and linoleyl alcohol oxidation catalyzed by 5-lipoxygenase].

PubMed

Kharchenko, O V; Kharitonenko, A I; Vovk, A I; Kukhar', V P; Babiĭ, L V; Khil'chevskiĭ, A N; Mel'nik, A K

2005-01-01

The inhibiting effects of 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO) and its 4-substituted derivatives in reactions of linoleyl acid or linoleyl alcohol oxidation catalyzed by potato tuber 5-lipoxygenase were investigated. Inhibiting properties of stable nitroxyl radicals in presence of lubrol and SDS were reduced at the transition from TEMPO to 4-hydroxy-TEMPO or 4-amino-TEMPO and increased at use of adamantane-1-carboxylic or 3-methyladamantane-1-carboxylic acid 1-oxyl-2,2,6,6-tetramethylpiperidine-4-yl esters. Enzyme activity at saturating concentrations of inhibitor was not suppressed completely, and decreased up to the certain level determined by the substrate nature. The dependence of partial inhibition efficiency on rotational correlation time of stable nitroxides in model micellar systems were analysed. It was supposed that 5-lipoxygenase inhibition includes the interaction of hydrophobic nitroxide with radical intermediate formed in enzymatic process.

H NMR studies of substrate hydrogen exchange reactions catalyzed by L-methionine gamma-lyase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Esaki, N.; Nakayama, T.; Sawada, S.

Hydrogen exchange reactions of various L-amino acids catalyzed by L-methionine gamma-lyase (EC 4.4.1.11) have been studied. The enzyme catalyzes the rapid exchange of the alpha- and beta-hydrogens of L-methionine and S-methyl-L-cysteine with deuterium from the solvent. The rate of alpha-hydrogen exchange was about 40 times faster than that of the enzymatic elimination reaction of the sulfur-containing amino acids. The enzyme also catalyzes the exchange reaction of alpha- and beta-hydrogens of the straight-chain L-amino acids which are not susceptible to elimination. The exchange rates of the alpha-hydrogen and the total beta-hydrogens of L-alanine and L-alpha-aminobutyrate with deuterium followed first-order kinetics. Formore » L-norvaline, L-norleucine, S-methyl-L-cysteine, and L-methionine, the rate of alpha-hydrogen exchange followed first-order kinetics, but the rate of total beta-hydrogen exchange decreased due to a primary isotope effect at the alpha-position. L-Phenylalanine and L-tryptophan slowly underwent alpha-hydrogen exchange. The pro-R hydrogen of glycine was deuterated stereospecifically.« less

Lipase-catalyzed enantioselective synthesis of (R,R)-lactide from alkyl lactate to produce PDLA (poly D-lactic acid) and stereocomplex PLA (poly lactic acid).

PubMed

Jeon, Byoung Wook; Lee, Jumin; Kim, Hyun Sook; Cho, Dae Haeng; Lee, Hyuk; Chang, Rakwoo; Kim, Yong Hwan

2013-10-20

R-lactide, a pivotal monomer for the production of poly (D-lactic acid) (PDLA) or stereocomplex poly (lactic acid) (PLA) was synthesized from alkyl (R)-lactate through a lipase-catalyzed reaction without racemization. From among several types of lipase, only lipase B from Candida antarctica (Novozym 435; CAL-B) was effective in the reaction that synthesized (R,R)-lactide. Enantiopure (R,R)-lactide, which consisted of over 99% enantiomeric excess, was synthesized from methyl (R)-lactate through CAL-B catalysis. Removal of the methanol by-product was critical to obtain a high level of lactide conversion. The (R,R)-lactide yield was 56% in a reaction containing 100 mg of Novozym 435, 10 mM methyl (R)-lactate and 1500 mg of molecular sieve 5A in methyl tert-butyl ether (MTBE). The important monomer (R,R)-lactide that is required for the production of the widely recognized bio-plastic PDLA and the PLA stereocomplex can be obtained using this novel synthetic method. Copyright © 2013 Elsevier B.V. All rights reserved.

Direct amidation of carboxylic acids catalyzed by ortho-iodo arylboronic acids: catalyst optimization, scope, and preliminary mechanistic study supporting a peculiar halogen acceleration effect.

PubMed

Gernigon, Nicolas; Al-Zoubi, Raed M; Hall, Dennis G

2012-10-05

The importance of amides as a component of biomolecules and synthetic products motivates the development of catalytic, direct amidation methods employing free carboxylic acids and amines that circumvent the need for stoichiometric activation or coupling reagents. ortho-Iodophenylboronic acid 4a has recently been shown to catalyze direct amidation reactions at room temperature in the presence of 4A molecular sieves as dehydrating agent. Herein, the arene core of ortho-iodoarylboronic acid catalysts has been optimized with regards to the electronic effects of ring substitution. Contrary to the expectation, it was found that electron-donating substituents are preferable, in particular, an alkoxy substituent positioned para to the iodide. The optimal new catalyst, 5-methoxy-2-iodophenylboronic acid (MIBA, 4f), was demonstrated to be kinetically more active than the parent des-methoxy catalyst 4a, providing higher yields of amide products in shorter reaction times under mild conditions at ambient temperature. Catalyst 4f is recyclable and promotes the formation of amides from aliphatic carboxylic acids and amines, and from heteroaromatic carboxylic acids and other functionalized substrates containing moieties like a free phenol, indole and pyridine. Mechanistic studies demonstrated the essential role of molecular sieves in this complex amidation process. The effect of substrate stoichiometry, concentration, and measurement of the catalyst order led to a possible catalytic cycle based on the presumed formation of an acylborate intermediate. The need for an electronically enriched ortho-iodo substituent in catalyst 4f supports a recent theoretical study (Marcelli, T. Angew. Chem. Int. Ed.2010, 49, 6840-6843) with a purported role for the iodide as a hydrogen-bond acceptor in the orthoaminal transition state.

Effect of polyvinylpyrrolidone on mesoporous silica morphology and esterification of lauric acid with 1-butanol catalyzed by immobilized enzyme

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Jinyu; Zhou, Guowei, E-mail: guoweizhou@hotmail.com; Jiang, Bin

2014-05-01

Mesoporous silica materials with a range of morphology evolution, i.e., from curved rod-shaped mesoporous silica to straight rod-shaped mesoporous silica, were successfully prepared using polyvinylpyrrolidone (PVP) and triblock copolymer as dual template. The effects of PVP molecular weight and concentration on mesoporous silica structure parameters were studied. Results showed that surface area and pore volume continuously decreased with increased PVP molecular weight. Mesoporous silica prepared with PVP K30 also possessed larger pore diameter, interplanar spacing (d{sub 100}), and cell parameter (a{sub 0}) than that prepared with PVP K15 and PVP K90. In addition, with increased PVP concentration, d{sub 100} andmore » a{sub 0} continuously decreased. The mechanism of morphology evolution caused by the change in PVP concentration was investigated. The conversion rate of lauric acid with 1-butanol catalyzed by immobilized Porcine pancreatic lipase (PPL) was also evaluated. Results showed that PPL immobilized on amino-functionalized straight rod-shaped mesoporous silica maintained 50% of its esterification conversion rate even after five cycles of use with a maximum conversion rate was about 90.15%. - Graphical abstract: Curved rod-shaped mesoporous silica can be obtained at low and the highest PVP concentration, while straight rod-shaped mesoporous silica can be obtained at higher PVP concentration. - Highlights: • Mesoporous silica with morphology evolution from CRMS to SRMS were prepared. • Effects of PVP molecular weight and concentration on silica morphology were studied. • A possible mechanism for the formation of morphology evolution SiO{sub 2} was proposed. • Esterification of lauric acid with 1-butanol catalyzed by immobilized PPL.« less

Phosphine-Catalyzed Doubly Stereoconvergent γ-Additions of Racemic Heterocycles to Racemic Allenoates: The Catalytic Enantioselective Synthesis of Protected α,α-Disubstituted α-Amino Acid Derivatives.

PubMed

Kalek, Marcin; Fu, Gregory C

2015-07-29

Methods have recently been developed for the phosphine-catalyzed asymmetric γ-addition of nucleophiles to readily available allenoates and alkynoates to generate useful α,β-unsaturated carbonyl compounds that bear a stereogenic center in either the γ or the δ position (but not both) with high stereoselectivity. The utility of this approach would be enhanced considerably if the stereochemistry at both termini of the new bond could be controlled effectively. In this report, we describe the achievement of this objective, specifically, that a chiral phosphepine can catalyze the stereoconvergent γ-addition of a racemic nucleophile to a racemic electrophile; through the choice of an appropriate heterocycle as the nucleophilic partner, this new method enables the synthesis of protected α,α-disubstituted α-amino acid derivatives in good yield, diastereoselectivity, and enantioselectivity.

Acid- and base-catalysis in the mononuclear rearrangement of some (Z)-arylhydrazones of 5-amino-3-benzoyl-1,2,4-oxadiazole in toluene: effect of substituents on the course of reaction.

PubMed

D'Anna, Francesca; Frenna, Vincenzo; Ghelfi, Franco; Marullo, Salvatore; Spinelli, Domenico

2011-04-15

The reaction rates for the rearrangement of eleven (Z)-arylhydrazones of 5-amino-3-benzoyl-1,2,4-oxadiazole 3a-k into the relevant (2-aryl-5-phenyl-2H-1,2,3-triazol-4-yl)ureas 4a-k in the presence of trichloroacetic acid or of piperidine have been determined in toluene at 313.1 K. The results have been related to the effect of the aryl substituent by using Hammett and/or Ingold-Yukawa-Tsuno correlations and have been compared with those previously collected in a protic polar solvent (dioxane/water) as well as with those on the analogous rearrangement of the corresponding (Z)-arylhydrazones of 3-benzoyl-5-phenyl-1,2,4-oxadiazole 1a-k in benzene. Some light can thus be shed on the general differences of chemical reactivity between protic polar (or dipolar aprotic) and apolar solvents.

Heteropoly acid-catalyzed microwave-assisted three-component aza-Diels-Alder cyclizations: diastereoselective synthesis of potential drug candidates for Alzheimer's disease.

PubMed

Borkin, Dmitry; Morzhina, Elena; Datta, Silpi; Rudnitskaya, Aleksandra; Sood, Abha; Török, Marianna; Török, Béla

2011-03-07

A highly diastereoselective microwave-assisted three component synthesis of azabicyclo[2.2.2]octan-5-ones by a silicotungstic acid-catalyzed aza-Diels-Alder cyclization is described. The one-pot process involves the formation of the in situ generated Schiff base and its immediate cyclization with cyclohex-2-enone. The short reaction times, good yields and excellent diastereoselectivity make this annulation a practical and environmentally attractive method for the synthesis of the target compounds. Preliminary assays were carried out to determine the activity of the products in AChE as well as in amyloid β fibrillogenesis inhibition.

Conversion of nicotinic acid to trigonelline is catalyzed by N-methyltransferase belonged to motif B′ methyltransferase family in Coffea arabica

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mizuno, Kouichi, E-mail: koumno@akita-pu.ac.jp; Matsuzaki, Masahiro; Kanazawa, Shiho

Graphical abstract: Trigonelline synthase catalyzes the conversion of nicotinic acid to trigonelline. We isolated and characterized trigonelline synthase gene(s) from Coffea arabica. - Highlights: • Trigonelline is a major compound in coffee been same as caffeine is. • We isolated and characterized trigonelline synthase gene. • Coffee trigonelline synthases are highly homologous with coffee caffeine synthases. • This study contributes the fully understanding of pyridine alkaloid metabolism. - Abstract: Trigonelline (N-methylnicotinate), a member of the pyridine alkaloids, accumulates in coffee beans along with caffeine. The biosynthetic pathway of trigonelline is not fully elucidated. While it is quite likely that themore » production of trigonelline from nicotinate is catalyzed by N-methyltransferase, as is caffeine synthase (CS), the enzyme(s) and gene(s) involved in N-methylation have not yet been characterized. It should be noted that, similar to caffeine, trigonelline accumulation is initiated during the development of coffee fruits. Interestingly, the expression profiles for two genes homologous to caffeine synthases were similar to the accumulation profile of trigonelline. We presumed that these two CS-homologous genes encoded trigonelline synthases. These genes were then expressed in Escherichiacoli, and the resulting recombinant enzymes that were obtained were characterized. Consequently, using the N-methyltransferase assay with S-adenosyl[methyl-{sup 14}C]methionine, it was confirmed that these recombinant enzymes catalyzed the conversion of nicotinate to trigonelline, coffee trigonelline synthases (termed CTgS1 and CTgS2) were highly identical (over 95% identity) to each other. The sequence homology between the CTgSs and coffee CCS1 was 82%. The pH-dependent activity curve of CTgS1 and CTgS2 revealed optimum activity at pH 7.5. Nicotinate was the specific methyl acceptor for CTgSs, and no activity was detected with any other nicotinate

Computational Insights into an Enzyme-Catalyzed [4+2] Cycloaddition

PubMed Central

2017-01-01

The enzyme SpnF, involved in the biosynthesis of spinosyn A, catalyzes a formal [4+2] cycloaddition of a 22-membered macrolactone, which may proceed as a concerted [4+2] Diels–Alder reaction or a stepwise [6+4] cycloaddition followed by a Cope rearrangement. Quantum mechanics/molecular mechanics (QM/MM) calculations combined with free energy simulations show that the Diels–Alder pathway is favored in the enzyme environment. OM2/CHARMM free energy simulations for the SpnF-catalyzed reaction predict a free energy barrier of 22 kcal/mol for the concerted Diels–Alder process and provide no evidence of a competitive stepwise pathway. Compared with the gas phase, the enzyme lowers the Diels–Alder barrier significantly, consistent with experimental observations. Inspection of the optimized geometries indicates that the enzyme may prearrange the substrate within the active site to accelerate the [4+2] cycloaddition and impede the [6+4] cycloaddition through interactions with active-site residues. Judging from partial charge analysis, we find that the hydrogen bond between the Thr196 residue of SpnF and the substrate C15 carbonyl group contributes to the enhancement of the rate of the Diels–Alder reaction. QM/MM simulations show that the substrate can easily adopt a reactive conformation in the active site of SpnF because interconversion between the C5–C6 s-trans and s-cis conformers is facile. Our QM/MM study suggests that the enzyme SpnF does behave as a Diels-Alderase. PMID:29131960

A chiral Brønsted acid-catalyzed highly enantioselective Mannich-type reaction of α-diazo esters with in situ generated N-acyl ketimines.

PubMed

Unhale, Rajshekhar A; Sadhu, Milon M; Ray, Sumit K; Biswas, Rayhan G; Singh, Vinod K

2018-04-03

A chiral phosphoric acid-catalyzed asymmetric Mannich-type reaction of α-diazo esters with in situ generated N-acyl ketimines, derived from 3-hydroxyisoindolinones has been demonstrated in this communication. A variety of isoindolinone-based α-amino diazo esters bearing a quaternary stereogenic center were afforded in high yields (up to 99%) with excellent enantioselectivities (up to 99% ee). Furthermore, the synthetic utility of the products has been depicted by the hydrogenation of the diazo moiety of adducts.

One-step production of biodiesel from rice bran oil catalyzed by chlorosulfonic acid modified zirconia via simultaneous esterification and transesterification.

PubMed

Zhang, Yue; Wong, Wing-Tak; Yung, Ka-Fu

2013-11-01

Due to the high content (25-50%) of free fatty acid (FFA), crude rice bran oil usually requires a two steps conversion or one step conversion with very harsh condition for simultaneous esterification and transesterification. In this study, chlorosulfonic acid modified zirconia (HClSO3-ZrO2) with strong acidity and durability is prepared and it shows excellent catalytic activity toward simultaneous esterification and transesterification. Under a relative low reaction temperature of 120 °C, HClSO3-ZrO2 catalyzes a complete conversion of simulated crude rice bran oil (refined oil with 40 wt% FFA) into biodiesel and the conversion yield keep at above 92% for at least three cycles. Further investigation on the tolerance towards FFA and water reveals that it maintains high activity even with the presence of 40 wt% FFA and 3 wt% water. It shows that HClSO3-ZrO2 is a robust and durable catalyst which shows high potential to be commercial catalyst for biodiesel production from low grade feedstock. Copyright © 2013 Elsevier Ltd. All rights reserved.

Inspiring Examples in Rearrangements of Infinite Products

ERIC Educational Resources Information Center

Ramasinghe, W.

2007-01-01

It is well known that simple examples are really encouraging in the understanding of rearrangements of infinite series. In this paper a similar role is played by simple examples in the case of infinite products. Iterated products of double products seem to have a similar spirit of rearrangements of products, although they are not the same.…

Spectroscopic investigation of H atom transfer in a gas-phase dissociation reaction: McLafferty rearrangement of model gas-phase peptide ions.

PubMed

Van Stipdonk, Michael J; Kerstetter, Dale R; Leavitt, Christopher M; Groenewold, Gary S; Steill, Jeffrey; Oomens, Jos

2008-06-14

Wavelength-selective infrared multiple-photon photodissociation (WS-IRMPD) was used to study isotopically-labeled ions generated by McLafferty rearrangement of nicotinyl-glycine-tert-butyl ester and betaine-glycine-tert-butyl ester. The tert-butyl esters were incubated in a mixture of D(2)O and CH(3)OD to induce solution-phase hydrogen-deuterium exchange and then converted to gas-phase ions using electrospray ionization. McLafferty rearrangement was used to generate the free-acid forms of the respective model peptides through transfer of an H atom and elimination of butene. The specific aim was to use vibrational spectra generated by WS-IRMPD to determine whether the H atom remains at the acid group, or migrates to one or more of the other exchangeable sites. Comparison of the IRMPD results in the region from 1200-1900 cm(-1) to theoretical spectra for different isotopically-labeled isomers clearly shows that the H atom is situated at the C-terminal acid group and migration to amide positions is negligible on the time scale of the experiment. The results of this study suggest that use of the McLafferty rearrangement for peptide esters could be an effective approach for generation of H-atom isotope tracers, in situ, for subsequent investigation of intramolecular proton migration during peptide fragmentation studies.

Nuclear positioning rather than contraction controls ordered rearrangements of immunoglobulin loci.

PubMed

Rother, Magdalena B; Palstra, Robert-Jan; Jhunjhunwala, Suchit; van Kester, Kevin A M; van IJcken, Wilfred F J; Hendriks, Rudi W; van Dongen, Jacques J M; Murre, Cornelis; van Zelm, Menno C

2016-01-08

Progenitor-B cells recombine their immunoglobulin (Ig) loci to create unique antigen receptors. Despite a common recombination machinery, the Ig heavy and Ig light chain loci rearrange in a stepwise manner. We studied pre-pro-B cells and Rag(-/-) progenitor-B cells to determine whether Ig locus contraction or nuclear positioning is decisive for stepwise rearrangements. We found that both Ig loci were contracted in pro-B and pre-B cells. Igh relocated from the nuclear lamina to central domains only at the pro-B cell stage, whereas, Igκ remained sequestered at the lamina, and only at the pre-B cell stage located to central nuclear domains. Finally, in vitro induced re-positioning of Ig alleles away from the nuclear periphery increased germline transcription of Ig loci in pre-pro-B cells. Thus, Ig locus contraction juxtaposes genomically distant elements to mediate efficient recombination, however, sequential positioning of Ig loci away from the nuclear periphery determines stage-specific accessibility of Ig loci. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Human, Mouse, and Rat Genome Large-Scale Rearrangements: Stability Versus Speciation

PubMed Central

Zhao, Shaying; Shetty, Jyoti; Hou, Lihua; Delcher, Arthur; Zhu, Baoli; Osoegawa, Kazutoyo; de Jong, Pieter; Nierman, William C.; Strausberg, Robert L.; Fraser, Claire M.

2004-01-01

Using paired-end sequences from bacterial artificial chromosomes, we have constructed high-resolution synteny and rearrangement breakpoint maps among human, mouse, and rat genomes. Among the >300 syntenic blocks identified are segments of over 40 Mb without any detected interspecies rearrangements, as well as regions with frequently broken synteny and extensive rearrangements. As closely related species, mouse and rat share the majority of the breakpoints and often have the same types of rearrangements when compared with the human genome. However, the breakpoints not shared between them indicate that mouse rearrangements are more often interchromosomal, whereas intrachromosomal rearrangements are more prominent in rat. Centromeres may have played a significant role in reorganizing a number of chromosomes in all three species. The comparison of the three species indicates that genome rearrangements follow a path that accommodates a delicate balance between maintaining a basic structure underlying all mammalian species and permitting variations that are necessary for speciation. PMID:15364903

Rearrangement moves on rooted phylogenetic networks

PubMed Central

Gambette, Philippe; van Iersel, Leo; Jones, Mark; Scornavacca, Celine

2017-01-01

Phylogenetic tree reconstruction is usually done by local search heuristics that explore the space of the possible tree topologies via simple rearrangements of their structure. Tree rearrangement heuristics have been used in combination with practically all optimization criteria in use, from maximum likelihood and parsimony to distance-based principles, and in a Bayesian context. Their basic components are rearrangement moves that specify all possible ways of generating alternative phylogenies from a given one, and whose fundamental property is to be able to transform, by repeated application, any phylogeny into any other phylogeny. Despite their long tradition in tree-based phylogenetics, very little research has gone into studying similar rearrangement operations for phylogenetic network—that is, phylogenies explicitly representing scenarios that include reticulate events such as hybridization, horizontal gene transfer, population admixture, and recombination. To fill this gap, we propose “horizontal” moves that ensure that every network of a certain complexity can be reached from any other network of the same complexity, and “vertical” moves that ensure reachability between networks of different complexities. When applied to phylogenetic trees, our horizontal moves—named rNNI and rSPR—reduce to the best-known moves on rooted phylogenetic trees, nearest-neighbor interchange and rooted subtree pruning and regrafting. Besides a number of reachability results—separating the contributions of horizontal and vertical moves—we prove that rNNI moves are local versions of rSPR moves, and provide bounds on the sizes of the rNNI neighborhoods. The paper focuses on the most biologically meaningful versions of phylogenetic networks, where edges are oriented and reticulation events clearly identified. Moreover, our rearrangement moves are robust to the fact that networks with higher complexity usually allow a better fit with the data. Our goal is to provide a

Acetylation of bacterial cellulose catalyzed by citric acid: Use of reaction conditions for tailoring the esterification extent.

PubMed

Ávila Ramírez, Jhon Alejandro; Gómez Hoyos, Catalina; Arroyo, Silvana; Cerrutti, Patricia; Foresti, María Laura

2016-11-20

Bacterial cellulose (BC) nanoribbons were partially acetylated by a simple direct solvent-free route catalyzed by citric acid. The assay of reaction conditions within chosen intervals (i.e. esterification time (0.5-7h), catalyst content (0.08-1.01mmol/mmol AGU), and temperature (90-140°C)), illustrated the flexibility of the methodology proposed, with reaction variables which can be conveniently manipulated to acetylate BC to the required degree of substitution (DS) within the 0.20-0.73 interval. Within this DS interval, characterization results indicated a surface-only process in which acetylated bacterial cellulose with tunable DS, preserved fibrous structure and increased hydrophobicity could be easily obtained. The feasibility of reusing the catalyst/excess acylant in view of potential scale-up was also illustrated. Copyright © 2016 Elsevier Ltd. All rights reserved.

Synthesis and characterization of poly(lactic acid)/ montmorillonite nanocomposites by in situ polycondensation catalyzed by non-metal-based compound.

PubMed

Kaewprapan, Kulwadee; Phattanarudee, Siriwan

2012-01-01

Poly(lactic acid)/montmorillonite nanocomposites were prepared by using non-toxic catalysts, i.e., phthalic acid and succinimide, via in situ polycondensation in presence of silicate. Concentrations of catalysts and clay were varied in a range of 0-3% wt and 0-0.5% wt, respectively. The reaction condition was controlled at 180 degrees C for 24 hr under a reduced pressure. Viscosity average molecular weight of the synthesized polymers and nanocomposites were characterized and compared using an Ubbelohde viscometer. Pattern of silicate distribution in the composites was investigated by X-ray diffraction to correlate with thermal properties evaluated by differential scanning calorimetry and thermogravimetric analysis. The results showed that the addition of catalysts at 2% wt gave the highest product yield (55-60%). The presence of silicate affected on molecular weight reduction, and the diffracted patterns suggested an intercalated structure. With a small amount of added filler, a significant improvement in thermal property and crystallinity of the resultant composites was obtained compared to those of the catalyzed polymers, in which the composites with succinimide exhibited overall better thermal stability and higher crystallinity than the ones prepared with phthalic acid.

Genome rearrangement shapes Prochlorococcus ecological adaptation.

PubMed

Yan, Wei; Wei, Shuzhen; Wang, Qiong; Xiao, Xilin; Zeng, Qinglu; Jiao, Nianzhi; Zhang, Rui

2018-06-18

Prochlorococcus is the most abundant and smallest known free-living photosynthetic microorganism and is a key player in marine ecosystems and biogeochemical cycles. Prochlorococcus can be broadly divided into high-light-adapted (HL) and low-light-adapted (LL) clades. In this study, we isolated two low-light-adapted I (LLI) strains from the western Pacific Ocean and obtained their genomic data. We reconstructed Prochlorococcus evolution based on genome rearrangement. Our results showed that genome rearrangement might have played an important role in Prochlorococcus evolution. We also found that the Prochlorococcus clades with streamlined genomes maintained relatively high synteny throughout most of their genomes, and several regions served as rearrangement hotspots. Backbone analysis showed that different clades shared a conserved backbone but also had clade-specific regions, and the genes in these regions were associated with ecological adaptations. Importance Prochlorococcus , the most abundant and smallest known free-living photosynthetic microorganism, play a key role in marine ecosystems and biogeochemical cycles. The Prochlorococcus genome evolution is a fundamental question related to how Prochlorococcus clades adapted to different ecological niches. Recent studies revealed that the gene gain and loss is crucial to the clade differentiation. The significance of our research is that we interpreted the Prochlorococcus genome evolution from the perspective of genome structure, and associated the genome rearrangement with the Prochlorococcus clade differentiation and subsequent ecological adaptation. Copyright © 2018 Yan et al.

A system for the detection of chromosomal rearrangements using Sordaria macrospora.

PubMed

Arnaise, S; Leblon, G; Lares, L

1984-01-01

A system is described for the detection and diagnosis of induced chromosomal rearrangement using Sordaria macrospora. The system uses the property of the rearrangement to produce defective white ascospores as meiotic progeny from heterozygous crosses. Two reconstruction experiments have shown that this system is able to give reliable quantitative measures of rearrangement frequencies. Evidence for a photoreactivation process was obtained, suggesting that pyrimidine dimers may well be an important lesion in UV-induced chromosomal rearrangement. No evidence of induction of chromosomal rearrangement was obtained in experiments with the powerful chemical mutagen N-methyl-N'-nitro-N-nitrosoguanidine.

Solvent effects in acid-catalyzed dehydration of the Diels-Alder cycloadduct between 2,5-dimethylfuran and maleic anhydride

NASA Astrophysics Data System (ADS)

Salavati-fard, Taha; Caratzoulas, Stavros; Doren, Douglas J.

2017-03-01

Dehydration of the cycloadduct produced from the Diels-Alder reaction between 2,5-dimethylfuran and maleic anhydride to 3,6-dimethylphthalic anhydride exemplifies an important step in producing platform chemicals from biomass. The mechanisms of dehydration and catalytic effects of Lewis and Brønsted acids are investigated with density functional theory. The uncatalyzed reaction has a very high activation barrier (68.7 kcal/mol) in the gas phase and it is not significantly affected by solvation. With a Lewis acid catalyst, modeled as an alkali ion, the activation barriers are reduced, but intermediates are also stabilized. The net effect in vacuum is that the energetic span, or apparent activation energy of the catalytic cycle, is 77.9 kcal/mol, even higher than the barrier in the uncatalyzed case. In solution, however, the energetic span is reduced by as much as 20 kcal/mol, due to differences in the solvation energy of the transition states and intermediates. In the case of a Brønsted acid catalyst, modeled as a proton, the gas phase transition state energies are reduced even more than in the Lewis acid case, and there is no strong stabilization of the intermediates. The energetic span in vacuum is only 13.8 kcal/mol and is reduced even further in solution. Brønsted acid catalysis appears to be the preferred mechanism for dehydration of this cycloadduct. Since the Diels-Alder reaction that produced the molecule has previously been shown to be catalyzed by Brønsted acids, this suggests that a single catalyst could be used to accelerate both steps.

15-Hydroxygermacranolides as Sources of Structural Diversity: Synthesis of Sesquiterpene Lactones by Cyclization and Rearrangement Reactions. Experimental and DFT Study.

PubMed

Álvarez-Calero, José María; Ruiz, Enrique; López-Pérez, José Luis; Jaraíz, Martín; Rubio, José E; Jorge, Zacarías D; Suárez, Margarita; Massanet, Guillermo M

2018-05-18

A study on the electrophile-induced rearrangement of two 15-hydroxygermacranolides, salonitenolide and artemisiifolin, was carried out. These compounds underwent electrophilic intramolecular cyclizations or acid-mediated rearrangements to give sesquiterpene lactones with different skeletons such as eudesmanolides, guaianolides, amorphanolides, or other germacranolides. The cyclization that gives guaianolides can be considered a biomimetic route to this type of sesquiterpene lactones. The use of acetone as a solvent changes the reactivity of the two starting germacranolides to the acid catalysts, with a 4,15-diol acetonide being the main product obtained. The δ-amorphenolide obtained by intramolecular cyclization of this acetonide is a valuable intermediate for accessing the antimalarials artemisinin and its derivatives. Mechanistic proposals for the transformations are raised, and to provide support them, quantum chemical calculations [DFT B3LYP/6-31+G(d,p) level] were undertaken.

Neural network for control of rearrangeable Clos networks.

PubMed

Park, Y K; Cherkassky, V

1994-09-01

Rapid evolution in the field of communication networks requires high speed switching technologies. This involves a high degree of parallelism in switching control and routing performed at the hardware level. The multistage crossbar networks have always been attractive to switch designers. In this paper a neural network approach to controlling a three-stage Clos network in real time is proposed. This controller provides optimal routing of communication traffic requests on a call-by-call basis by rearranging existing connections, with a minimum length of rearrangement sequence so that a new blocked call request can be accommodated. The proposed neural network controller uses Paull's rearrangement algorithm, along with the special (least used) switch selection rule in order to minimize the length of rearrangement sequences. The functional behavior of our model is verified by simulations and it is shown that the convergence time required for finding an optimal solution is constant, regardless of the switching network size. The performance is evaluated for random traffic with various traffic loads. Simulation results show that applying the least used switch selection rule increases the efficiency in switch rearrangements, reducing the network convergence time. The implementation aspects are also discussed to show the feasibility of the proposed approach.

Rearrangement of Retinogeniculate Projection Patterns after Eye-Specific Segregation in Mice

PubMed Central

Hayakawa, Itaru; Kawasaki, Hiroshi

2010-01-01

It has been of interest whether and when the rearrangement of neuronal circuits can be induced after projection patterns are formed during development. Earlier studies using cats reported that the rearrangement of retinogeniculate projections could be induced even after eye-specific segregation has occurred, but detailed and quantitative characterization of this rearrangement has been lacking. Here we delineate the structural changes of retinogeniculate projections in the C57BL/6 mouse in response to monocular enucleation (ME) after eye-specific segregation. When ME was performed after eye-specific segregation, rearrangement of retinogeniculate axons in the dorsal lateral geniculate nucleus (dLGN) was observed within 5 days. Although this rearrangement was observed both along the dorsomedial-ventrolateral and outer-inner axes in the dLGN, it occurred more rapidly along the outer-inner axis. We also examined the critical period for this rearrangement and found that the rearrangement became almost absent by the beginning of the critical period for ocular dominance plasticity in the primary visual cortex. Taken together, our findings serve as a framework for the assessment of phenotypes of genetically altered mouse strains as well as provide insights into the mechanisms underlying the rearrangement of retinogeniculate projections. PMID:20544023

Thermodynamics of enzyme-catalyzed esterifications: II. Levulinic acid esterification with short-chain alcohols.

PubMed

Altuntepe, Emrah; Emel'yanenko, Vladimir N; Forster-Rotgers, Maximilian; Sadowski, Gabriele; Verevkin, Sergey P; Held, Christoph

2017-10-01

Levulinic acid was esterified with methanol, ethanol, and 1-butanol with the final goal to predict the maximum yield of these equilibrium-limited reactions as function of medium composition. In a first step, standard reaction data (standard Gibbs energy of reaction Δ R g 0 ) were determined from experimental formation properties. Unexpectedly, these Δ R g 0 values strongly deviated from data obtained with classical group contribution methods that are typically used if experimental standard data is not available. In a second step, reaction equilibrium concentrations obtained from esterification catalyzed by Novozym 435 at 323.15 K were measured, and the corresponding activity coefficients of the reacting agents were predicted with perturbed-chain statistical associating fluid theory (PC-SAFT). The so-obtained thermodynamic activities were used to determine Δ R g 0 at 323.15 K. These results could be used to cross-validate Δ R g 0 from experimental formation data. In a third step, reaction-equilibrium experiments showed that equilibrium position of the reactions under consideration depends strongly on the concentration of water and on the ratio of levulinic acid: alcohol in the initial reaction mixtures. The maximum yield of the esters was calculated using Δ R g 0 data from this work and activity coefficients of the reacting agents predicted with PC-SAFT for varying feed composition of the reaction mixtures. The use of the new Δ R g 0 data combined with PC-SAFT allowed good agreement to the measured yields, while predictions based on Δ R g 0 values obtained with group contribution methods showed high deviations to experimental yields.

Atomic Rearrangements in Electron Attachment to Laser-Excited Molecules^*

NASA Astrophysics Data System (ADS)

Pinnaduwage, Lal; McCorkle, Dennis

1996-10-01

We report the observation of extensive atomic rearrangements in dissociative electron attachment to triethylamine " (Pinnaduwage and McCorkle, Chem.Phys. Lett. (in press, 1996))" and benzene laser excited to energies above their ionization thresholds. Large signal of "rearranged" negative ions, such as C_3^- (which is observed in both cases), were observed. This is in contrast to negative-ion formation via electron attachment to molecules in their ground states, where "rearranged" negative ions are comparatively weak and have been observed only occasionally. However, formation of "rearranged" positive ions is of common occurrence in the ionization of polyatomic molecules; it is possible that the formation of "rearranged" positive ions in the ionization processes, and the formation of such negative ions via electron attachment to excited states located close to the ionization threshold, are related. * Work supported by the LDRD Program of the Oak Ridge National Laboratory, managed by Lockheed Martin Energy Research Corp. for the US Department of Energy under contract number DE-AC05-96OR22464, and by the National Science Foundation under contract CHE-93113949 with the Univ. of Tenn., Knoxville.

Ruthenium-catalyzed alkylation of indoles with tertiary amines by oxidation of a sp3 C-H bond and Lewis acid catalysis.

PubMed

Wang, Ming-Zhong; Zhou, Cong-Ying; Wong, Man-Kin; Che, Chi-Ming

2010-05-17

Ruthenium porphyrins (particularly [Ru(2,6-Cl(2)tpp)CO]; tpp=tetraphenylporphinato) and RuCl(3) can act as oxidation and/or Lewis acid catalysts for direct C-3 alkylation of indoles, giving the desired products in high yields (up to 82% based on 60-95% substrate conversions). These ruthenium compounds catalyze oxidative coupling reactions of a wide variety of anilines and indoles bearing electron-withdrawing or electron-donating substituents with high regioselectivity when using tBuOOH as an oxidant, resulting in the alkylation of N-arylindoles to 3-{[(N-aryl-N-alkyl)amino]methyl}indoles (yield: up to 82%, conversion: up to 95%) and the alkylation of N-alkyl or N-H indoles to 3-[p-(dialkylamino)benzyl]indoles (yield: up to 73%, conversion: up to 92%). A tentative reaction mechanism involving two pathways is proposed: an iminium ion intermediate may be generated by oxidation of an sp(3) C-H bond of the alkylated aniline by an oxoruthenium species; this iminium ion could then either be trapped by an N-arylindole (pathway A) or converted to formaldehyde, allowing a subsequent three-component coupling reaction of the in situ generated formaldehyde with an N-alkylindole and an aniline in the presence of a Lewis acid catalyst (pathway B). The results of deuterium-labeling experiments are consistent with the alkylation of N-alkylindoles via pathway B. The relative reaction rates of [Ru(2,6-Cl(2)tpp)CO]-catalyzed oxidative coupling reactions of 4-X-substituted N,N-dimethylanilines with N-phenylindole (using tBuOOH as oxidant), determined through competition experiments, correlate linearly with the substituent constants sigma (R(2)=0.989), giving a rho value of -1.09. This rho value and the magnitudes of the intra- and intermolecular deuterium isotope effects (k(H)/k(D)) suggest that electron transfer most likely occurs during the initial stage of the oxidation of 4-X-substituted N,N-dimethylanilines. Ruthenium-catalyzed three-component reaction of N-alkyl/N-H indoles

Methyl Ester Production via Heterogeneous Acid-Catalyzed Simultaneous Transesterification and Esterification Reactions

NASA Astrophysics Data System (ADS)

Indrayanah, S.; Erwin; Marsih, I. N.; Suprapto; Murwani, I. K.

2017-05-01

The heterogeneous acid catalysts (MgF2 and ZnF2) have been used to catalyze the simultaneous transesterification and esterification reactions of crude palm oil (CPO) with methanol. Catalysts were synthesized by sol-gel method (combination of fluorolysis and hydrolysis). The physicochemical, structural, textural, thermal stability of the prepared catalysts was investigated by N2 adsorption-desorption, XRD, FT-IR, SEM and TG/DTG. Both MgF2 and ZnF2 have rutile structures with a different phase. The surface area of ZnF2 is smaller than that of MgF2, but the pore size and volume of ZnF2 are larger than those of MgF2. However, these materials are thermally stable. The performance of the catalysts is determined from the yield of catalysts toward the formation of methyl ester determined based on the product of methyl ester obtained from the reaction. The catalytic activity of ZnF2 is higher than MgF2 amounted to 85.21% and 26.82% with the optimum condition. The high activity of ZnF2 could be attributed to its pore diameter and pore volume but was not correlated with its surface area. The yield of methyl ester decreased along with the increase in molar ratio of methanol/CPO from 85.21 to 80.99 for ZnF2, respectively.

Muon Catalyzed Fusion

NASA Technical Reports Server (NTRS)

Armour, Edward A.G.

2007-01-01

Muon catalyzed fusion is a process in which a negatively charged muon combines with two nuclei of isotopes of hydrogen, e.g, a proton and a deuteron or a deuteron and a triton, to form a muonic molecular ion in which the binding is so tight that nuclear fusion occurs. The muon is normally released after fusion has taken place and so can catalyze further fusions. As the muon has a mean lifetime of 2.2 microseconds, this is the maximum period over which a muon can participate in this process. This article gives an outline of the history of muon catalyzed fusion from 1947, when it was first realised that such a process might occur, to the present day. It includes a description of the contribution that Drachrnan has made to the theory of muon catalyzed fusion and the influence this has had on the author's research.

An Enzyme-Catalyzed Multistep DNA Refolding Mechanism in Hairpin Telomere Formation

PubMed Central

Shi, Ke; Huang, Wai Mun; Aihara, Hideki

2013-01-01

Hairpin telomeres of bacterial linear chromosomes are generated by a DNA cutting–rejoining enzyme protelomerase. Protelomerase resolves a concatenated dimer of chromosomes as the last step of chromosome replication, converting a palindromic DNA sequence at the junctions between chromosomes into covalently closed hairpins. The mechanism by which protelomerase transforms a duplex DNA substrate into the hairpin telomeres remains largely unknown. We report here a series of crystal structures of the protelomerase TelA bound to DNA that represent distinct stages along the reaction pathway. The structures suggest that TelA converts a linear duplex substrate into hairpin turns via a transient strand-refolding intermediate that involves DNA-base flipping and wobble base-pairs. The extremely compact di-nucleotide hairpin structure of the product is fully stabilized by TelA prior to strand ligation, which drives the reaction to completion. The enzyme-catalyzed, multistep strand refolding is a novel mechanism in DNA rearrangement reactions. PMID:23382649

A complex, five breakpoint intrachromosomal rearrangement ascertained through two recombinant offspring

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tuck-Muller, C.M.; Li, Shibo; Chen, H.

Intrachromosomal rearrangements usually result from three or fewer breaks. We report a complex intrachromosomal rearrangement resulting from five breaks in one chromosome 10 of a phenotypically normal father of two developmentally delayed children. GTG-banding analysis of the father`s rearranged chromosome 10 suggested an initial pericentric inversion followed by an insertion from the short arm into the terminal band of the long arm. To our knowledge, this rearrangement is the most complex ever reported in a single chromosome. Both children inherited a recombinant chromosome 10 with loss of the insertion and the segment distal to it. Mechanisms for both rearrangements aremore » proposed. 7 refs., 2 figs.« less

Biodiesel from Citrullus colocynthis Oil: Sulfonic-Ionic Liquid-Catalyzed Esterification of a Two-Step Process

PubMed Central

Ali Elsheikh, Yasir; Hassan Akhtar, Faheem

2014-01-01

Biodiesel was prepared from Citrullus colocynthis oil (CCO) via a two-step process. The first esterification step was explored in two ionic liquids (ILs) with 1,3-disulfonic acid imidazolium hydrogen sulfate (DSIMHSO4) and 3-methyl-1-sulfonic acid imidazolium hydrogen sulfate (MSIMHSO4). Both ILs appeared to be good candidates to replace hazardous acidic catalyst due to their exceptional properties. However, the two sulfonic chains existing in DSIMHSO4 were found to increase the acidity to the IL than the single sulfonic chain in MSIMHSO4. Based on the results, 3.6 wt% of DSIMHSO4, methanol/CCO molar ratio of 12 : 1, and 150°C offered a final FFA conversion of 95.4% within 105 min. A 98.2% was produced via second KOH-catalyzed step in 1.0%, 6 : 1 molar ratio, 600 rpm, and 60°C for 50 min. This new two-step catalyzed process could solve the corrosion and environmental problems associated with the current acidic catalysts. PMID:24987736

Elucidation of Mechanisms and Selectivities of Metal-Catalyzed Reactions using Quantum Chemical Methodology.

PubMed

Santoro, Stefano; Kalek, Marcin; Huang, Genping; Himo, Fahmi

2016-05-17

Quantum chemical techniques today are indispensable for the detailed mechanistic understanding of catalytic reactions. The development of modern density functional theory approaches combined with the enormous growth in computer power have made it possible to treat quite large systems at a reasonable level of accuracy. Accordingly, quantum chemistry has been applied extensively to a wide variety of catalytic systems. A huge number of problems have been solved successfully, and vast amounts of chemical insights have been gained. In this Account, we summarize some of our recent work in this field. A number of examples concerned with transition metal-catalyzed reactions are selected, with emphasis on reactions with various kinds of selectivities. The discussed cases are (1) copper-catalyzed C-H bond amidation of indoles, (2) iridium-catalyzed C(sp(3))-H borylation of chlorosilanes, (3) vanadium-catalyzed Meyer-Schuster rearrangement and its combination with aldol- and Mannich-type additions, (4) palladium-catalyzed propargylic substitution with phosphorus nucleophiles, (5) rhodium-catalyzed 1:2 coupling of aldehydes and allenes, and finally (6) copper-catalyzed coupling of nitrones and alkynes to produce β-lactams (Kinugasa reaction). First, the methodology adopted in these studies is presented briefly. The electronic structure method in the great majority of these kinds of mechanistic investigations has for the last two decades been based on density functional theory. In the cases discussed here, mainly the B3LYP functional has been employed in conjunction with Grimme's empirical dispersion correction, which has been shown to improve the calculated energies significantly. The effect of the surrounding solvent is described by implicit solvation techniques, and the thermochemical corrections are included using the rigid-rotor harmonic oscillator approximation. The reviewed examples are chosen to illustrate the usefulness and versatility of the adopted methodology in

Palladium-catalyzed stereoretentive olefination of unactivated C(sp3)-H bonds with vinyl iodides at room temperature: synthesis of β-vinyl α-amino acids.

PubMed

Wang, Bo; Lu, Chengxi; Zhang, Shu-Yu; He, Gang; Nack, William A; Chen, Gong

2014-12-05

A method is reported for palladium-catalyzed N-quinolyl carboxamide-directed olefination of the unactivated C(sp(3))-H bonds of phthaloyl alanine with a broad range of vinyl iodides at room temperature. This reaction represents the first example of the stereoretentive installation of multisubstituted terminal and internal olefins onto unactivated C(sp(3))-H bonds. These methods enable access to a wide range of challenging β-vinyl α-amino acid products in a streamlined and controllable fashion, beginning from simple precursors.

Mechanistic Insight Facilitates Discovery of a Mild and Efficient Copper-Catalyzed Dehydration of Primary Amides to Nitriles Using Hydrosilanes.

PubMed

Liu, Richard Y; Bae, Minwoo; Buchwald, Stephen L

2018-02-07

Metal-catalyzed silylative dehydration of primary amides is an economical approach to the synthesis of nitriles. We report a copper-hydride(CuH)-catalyzed process that avoids a typically challenging 1,2-siloxane elimination step, thereby dramatically increasing the rate of the overall transformation relative to alternative metal-catalyzed systems. This new reaction proceeds at ambient temperature, tolerates a variety of metal-, acid-, or base-sensitive functional groups, and can be performed using a simple ligand, inexpensive siloxanes, and low catalyst loading.

The Aerobic Oxidation of Bromide to Dibromine Catalyzed by Homogeneous Oxidation Catalysts and Initiated by Nitrate in Acetic Acid

DOE Office of Scientific and Technical Information (OSTI.GOV)

Partenheimer, Walt; Fulton, John L.; Sorensen, Christina M.

A small amount of nitrate, ~0.002 molal, initiates the Co/Mn catalyzed aerobic oxidation of bromide compounds (HBr,NaBr,LiBr) to dibromine in acetic acid at room temperature. At temperatures 40oC or less , the reaction is autocatalytic. Co(II) and Mn(II) themselves and mixed with ionic bromide are known homogeneous oxidation catalysts. The reaction was discovered serendipitously when a Co/Br and Co/Mn/Br catalyst solution was prepared for the aerobic oxidation of methyaromatic compounds and the Co acetate contained a small amount of impurity i.e. nitrate. The reaction was characterized by IR, UV-VIS, MALDI and EXAFS spectroscopies and the coordination chemistry is described. Themore » reaction is inhibited by water and its rate changed by pH. The change in these variables, as well as others, are identical to those observed during homogeneous, aerobic oxidation of akylaromatics. A mechanism is proposed. Accidental addition of a small amount of nitrate compound into a Co/Mn/Br/acetic acid mixture in a large, commercial feedtank is potentially dangerous.« less

Iron Catalyzed Hydroformylation of Alkenes under Mild Conditions: Evidence of an Fe(II) Catalyzed Process.

PubMed

Pandey, Swechchha; Raj, K Vipin; Shinde, Dinesh R; Vanka, Kumar; Kashyap, Varchaswal; Kurungot, Sreekumar; Vinod, C P; Chikkali, Samir H

2018-03-28

Earth abundant, first row transition metals offer a cheap and sustainable alternative to the rare and precious metals. However, utilization of first row metals in catalysis requires harsh reaction conditions, suffers from limited activity, and fails to tolerate functional groups. Reported here is a highly efficient iron catalyzed hydroformylation of alkenes under mild conditions. This protocol operates at 10-30 bar syngas pressure below 100 °C, utilizes readily available ligands, and applies to an array of olefins. Thus, the iron precursor [HFe(CO) 4 ] - [Ph 3 PNPPh 3 ] + (1) in the presence of triphenyl phosphine catalyzes the hydroformylation of 1-hexene (S2), 1-octene (S1), 1-decene (S3), 1-dodecene (S4), 1-octadecene (S5), trimethoxy(vinyl)silane (S6), trimethyl(vinyl)silane (S7), cardanol (S8), 2,3-dihydrofuran (S9), allyl malonic acid (S10), styrene (S11), 4-methylstyrene (S12), 4- iBu-styrene (S13), 4- tBu-styrene (S14), 4-methoxy styrene (S15), 4-acetoxy styrene (S16), 4-bromo styrene (S17), 4-chloro styrene (S18), 4-vinylbenzonitrile (S19), 4-vinylbenzoic acid (S20), and allyl benzene (S21) to corresponding aldehydes in good to excellent yields. Both electron donating and electron withdrawing substituents could be tolerated and excellent conversions were obtained for S11-S20. Remarkably, the addition of 1 mol % acetic acid promotes the reaction to completion within 16-24 h. Detailed mechanistic investigations revealed in situ formation of an iron-dihydride complex [H 2 Fe(CO) 2 (PPh 3 ) 2 ] (A) as an active catalytic species. This finding was further supported by cyclic voltammetry investigations and intermediacy of an Fe(0)-Fe(II) species was established. Combined experimental and computational investigations support the existence of an iron-dihydride as the catalyst resting state, which then follows a Fe(II) based catalytic cycle to produce aldehyde.

Selective heterogeneous acid catalyzed esterification of N-terminal sulfyhdryl fatty acids

USDA-ARS?s Scientific Manuscript database

Our interest in thiol fatty acids lies in their antioxidative, free radical scavenging, and metal ion scavenging capabilities as applied to cosmeceutical and skin care formulations. The retail market is filled with products containing the disulfide-containing free fatty acid, lipoic acid. These pr...

Intrachromosomal Rearrangements in Rodents from the Perspective of Comparative Region-Specific Painting

PubMed Central

Serdyukova, Natalya A.; Perelman, Polina L.; Pavlova, Svetlana V.; Bulatova, Nina S.; Golenishchev, Feodor N.; Stanyon, Roscoe

2017-01-01

It has long been hypothesized that chromosomal rearrangements play a central role in different evolutionary processes, particularly in speciation and adaptation. Interchromosomal rearrangements have been extensively mapped using chromosome painting. However, intrachromosomal rearrangements have only been described using molecular cytogenetics in a limited number of mammals, including a few rodent species. This situation is unfortunate because intrachromosomal rearrangements are more abundant than interchromosomal rearrangements and probably contain essential phylogenomic information. Significant progress in the detection of intrachromosomal rearrangement is now possible, due to recent advances in molecular biology and bioinformatics. We investigated the level of intrachromosomal rearrangement in the Arvicolinae subfamily, a species-rich taxon characterized by very high rate of karyotype evolution. We made a set of region specific probes by microdissection for a single syntenic region represented by the p-arm of chromosome 1 of Alexandromys oeconomus, and hybridized the probes onto the chromosomes of four arvicolines (Microtus agrestis, Microtus arvalis, Myodes rutilus, and Dicrostonyx torquatus). These experiments allowed us to show the intrachromosomal rearrangements in the subfamily at a significantly higher level of resolution than previously described. We found a number of paracentric inversions in the karyotypes of M. agrestis and M. rutilus, as well as multiple inversions and a centromere shift in the karyotype of M. arvalis. We propose that during karyotype evolution, arvicolines underwent a significant number of complex intrachromosomal rearrangements that were not previously detected. PMID:28867774

Diastereoselective carbocyclization of 1,6-heptadienes triggered by rhodium-catalyzed activation of an olefinic C-H bond.

PubMed

Aïssa, Christophe; Ho, Kelvin Y T; Tetlow, Daniel J; Pin-Nó, María

2014-04-14

The use of α,ω-dienes as functionalization reagents for olefinic carbon-hydrogen bonds has been rarely studied. Reported herein is the rhodium(I)-catalyzed rearrangement of prochiral 1,6-heptadienes into [2,2,1]-cycloheptane derivatives with concomitant creation of at least three stereogenic centers and complete diastereocontrol. Deuterium-labeling studies and the isolation of a key intermediate are consistent with a group-directed C-H bond activation, followed by two consecutive migratory insertions, with only the latter step being diastereoselective. © 2014 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Ontogeny-Driven rDNA Rearrangement, Methylation, and Transcription, and Paternal Influence

PubMed Central

Shiao, Yih-Horng; Leighty, Robert M.; Wang, Cuiju; Ge, Xin; Crawford, Erik B.; Spurrier, Joshua M.; McCann, Sean D.; Fields, Janet R.; Fornwald, Laura; Riffle, Lisa; Driver, Craig; Quiñones, Octavio A.; Wilson, Ralph E.; Kasprzak, Kazimierz S.; Travlos, Gregory S.; Alvord, W. Gregory; Anderson, Lucy M.

2011-01-01

Gene rearrangement occurs during development in some cell types and this genome dynamics is modulated by intrinsic and extrinsic factors, including growth stimulants and nutrients. This raises a possibility that such structural change in the genome and its subsequent epigenetic modifications may also take place during mammalian ontogeny, a process undergoing finely orchestrated cell division and differentiation. We tested this hypothesis by comparing single nucleotide polymorphism-defined haplotype frequencies and DNA methylation of the rDNA multicopy gene between two mouse ontogenic stages and among three adult tissues of individual mice. Possible influences to the genetic and epigenetic dynamics by paternal exposures were also examined for Cr(III) and acid saline extrinsic factors. Variables derived from litters, individuals, and duplicate assays in large mouse populations were examined using linear mixed-effects model. We report here that active rDNA rearrangement, represented by changes of haplotype frequencies, arises during ontogenic progression from day 8 embryos to 6-week adult mice as well as in different tissue lineages and is modifiable by paternal exposures. The rDNA methylation levels were also altered in concordance with this ontogenic progression and were associated with rDNA haplotypes. Sperm showed highest level of methylation, followed by lungs and livers, and preferentially selected haplotypes that are positively associated with methylation. Livers, maintaining lower levels of rDNA methylation compared with lungs, expressed more rRNA transcript. In vitro transcription demonstrated haplotype-dependent rRNA expression. Thus, the genome is also dynamic during mammalian ontogeny and its rearrangement may trigger epigenetic changes and subsequent transcriptional controls, that are further influenced by paternal exposures. PMID:21765958

Application of a new amidophosphite ligand to Rh-catalyzed asymmetric hydrogenation of β-dehydroamino acid derivatives in supercritical carbon dioxide: activation effect of protic Co-solvents.

PubMed

Lyubimov, Sergey E; Rastorguev, Eugenie A; Davankov, Vadim A

2011-09-01

New chiral amidophosphite ligand was synthesized and tested in the Rh-catalyzed asymmetric hydrogenation of (Z)-β-(acylamino)acrylates in protic solvents and supercritical carbon dioxide (scCO(2) ) The catalytic performance is affected greatly by the acidity of the solvents. Better enantioselectivity (up to 88% ee) was achieved in scCO(2) containing 1,1,1,3,3,3-hexafluoro-2-propanol, compared to neat protic solvents. Copyright © 2011 Wiley-Liss, Inc.

Analysis of Expressed and Non-Expressed IGK Locus Rearrangements in Chronic Lymphocytic Leukemia

PubMed Central

Belessi, Chrysoula; Stamatopoulos, Kostas; Hadzidimitriou, Anastasia; Hatzi, Katerina; Smilevska, Tatjana; Stavroyianni, Niki; Marantidou, Fotini; Paterakis, George; Fassas, Athanasios; Anagnostopoulos, Achilles; Laoutaris, Nikolaos

2005-01-01

Immunoglobulin κ (IGK) locus rearrangements were analyzed in parallel on cDNA/genomic DNA in 188 κ- and 103 λ-chronic lymphocytic leukemia (CLL) cases. IGKV-KDE and IGKJ-C-intron-KDE rearrangements were also analyzed on genomic DNA. In κ-CLL, only 3 of 188 cases carried double in-frame IGKV-J transcripts: in such cases, the possibility that leukemic cells expressed more than one κ chain cannot be excluded. Twenty-eight κ-CLL cases also carried nonexpressed (nontranscribed and/or out-of-frame) IGKV-J rearrangements. Taking IGKV-J, IGKV-KDE, and IGKJ-C-intron-KDE rearrangements together, 38% of κ-CLL cases carried biallelic IGK locus rearrangements. In λ-CLL, 69 IGKV-J rearrangements were detected in 64 of 103 cases (62%); 24 rearrangements (38.2%) were in-frame. Four cases carried in-frame IGKV-J transcripts but retained monotypic light-chain expression, suggesting posttranscriptional regulation of allelic exclusion. In all, taking IGKV-J, IGKV-KDE, and IGKJ-C-intron-KDE rearrangements together, 97% of λ-CLL cases had at least 1 rearranged IGK allele, in keeping with normal cells. IG repertoire comparisons in κ- versus λ-CLL revealed that CLL precursor cells tried many rearrangements on the same IGK allele before they became λ producers. Thirteen of 28 and 26 of 69 non-expressed sequences in, respectively, κ- or λ-CLL had < 100% homology to germline. This finding might be considered as evidence for secondary rearrangements occurring after the onset of somatic hypermutation, at least in some cases. The inactivation of potentially functional IGKV-J joints by secondary rearrangements indicates active receptor editing in CLL and provides further evidence for the role of antigen in CLL immunopathogenesis. PMID:16622520

The Isomerization of (-)-Menthone to (+)-Isomenthone Catalyzed by an Ion-Exchange Resin

ERIC Educational Resources Information Center

Ginzburg, Aurora L.; Baca, Nicholas A.; Hampton, Philip D.

2014-01-01

A traditional organic chemistry laboratory experiment involves the acid-catalyzed isomerization of (-)-menthone to (+)-isomenthone. This experiment generates large quantities of organic and aqueous waste, and only allows the final ratio of isomers to be determined. A "green" modification has been developed that replaces the mineral acid…

An efficient synthesis of 3,4-Dihydropyrimidin-2(1H)-ones and thiones catalyzed by a novel Brønsted acidic ionic liquid under solvent-free conditions.

PubMed

Zhang, Yonghong; Wang, Bin; Zhang, Xiaomei; Huang, Jianbin; Liu, Chenjiang

2015-02-26

We report here an efficient and green method for Biginelli condensation reaction of aldehydes, β-ketoesters and urea or thiourea catalyzed by Brønsted acidic ionic liquid [Btto][p-TSA] under solvent-free conditions. Compared to the classical Biginelli reaction conditions, the present method has the advantages of giving good yields, short reaction times, near room temperature conditions and the avoidance of the use of organic solvents and metal catalyst.

10 CFR 2.909 - Rearrangement or suspension of proceedings.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Rearrangement or suspension of proceedings. 2.909 Section 2.909 Energy NUCLEAR REGULATORY COMMISSION RULES OF PRACTICE FOR DOMESTIC LICENSING PROCEEDINGS AND.../or National Security Information § 2.909 Rearrangement or suspension of proceedings. In any...

10 CFR 2.909 - Rearrangement or suspension of proceedings.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 1 2011-01-01 2011-01-01 false Rearrangement or suspension of proceedings. 2.909 Section 2.909 Energy NUCLEAR REGULATORY COMMISSION RULES OF PRACTICE FOR DOMESTIC LICENSING PROCEEDINGS AND.../or National Security Information § 2.909 Rearrangement or suspension of proceedings. In any...

Rearrangement of Immunoglobulin Genes in Shark Germ Cells

PubMed Central

Lee, Susan S.; Fitch, David; Flajnik, Martin F.; Hsu, Ellen

2000-01-01

The variable (V), (diversity [D]), and joining (J) region recombinases (recombination activating genes [RAGs]) can perform like transposases and are thought to have initiated development of the adaptive immune system in early vertebrates by splitting archaic V genes with transposable elements. In cartilaginous fishes, the immunoglobulin (Ig) light chain genes are organized as multiple VJ-constant (C) clusters; some loci are capable of rearrangement while others contain fused VJ. The latter may be key to understanding the evolutionary role of RAG. Are they relics of the archaic genes, or are they results of rearrangement in germ cells? Our data suggest that some fused VJ genes are not only recently rearranged, but also resulted from RAG-like activity involving hairpin intermediates. Expression studies show that these, like some other germline-joined Ig sequences, are expressed at significant levels only early in ontogeny. We suggest that a rejoined Ig gene may not merely be a sequence restricting antibody diversity, but is potentially a novel receptor no longer tied to somatic RAG expression and rearrangement. From the combined data, we arrived at the unexpected conclusion that, in some vertebrates, RAG is still an active force in changing the genome. PMID:10811858

Prostaglandin H synthase-catalyzed oxidation of all-trans- and 13-cis-retinoic acid to carbon-centered and peroxyl radical intermediates.

PubMed

Freyaldenhoven, M A; Lloyd, R V; Samokyszyn, V M

1996-06-01

Due to the importance of all-trans-retinoic acid (RA) in the treatment of various dermatological conditions and the wide distribution of prostaglandin H synthase (PGHS) in tissues, we have further examined the mechanisms involved in the hydroperoxide-dependent cooxidation of RA and its isomer, 13-cis-retinoic acid ((13Z)-RA), by PGHS. Hydroperoxide-dependent, PGHS-catalyzed oxidation of RA and (13Z)-RA was shown to form free radical adducts, using electron spin resonance (ESR) spin trapping techniques and 5-phenyl-4-penten-1-yl hydroperoxide (PPHP) or 13-hydroperoxy-9-cis-11-trans-octadecadienoic acid (13-OOH-18:2) as hydroperoxide substrates. Utilization of the spin trap alpha-phenyl-N-tert-butylnitrone (PBN) resulted in the detection of (13Z)-RA-PBN and RA-PBN adducts whose spectra were characterized by hyperfine coupling constants of aH = 4.16/aN = 15.69 and aH = 3.01/aN =15.92, respectively. Identical experiments under anaerobic conditions were carried out using the spin trap 2-methyl-2-nitrosopropane (NtB) which yielded nitroxide adducts whose spectra were characterized by a triplet of doublets with values of aH = 3.49/aN = 15.84 for the (13Z)-RA adduct and aH = 3.49/aN = 15.88 for the RA adduct. These results are indicative of secondary carbon-centered radical formation. We also used (+)-benzo[a]pyrene 7(S),8(S)-dihydrodiol ((+)-BP-7,8-diol) as a peroxyl radical probe. The results demonstrated the formation of (+)-BP-7,8-diol-derived tetrols, with the trans-anti tetrol representing the major oxidation product in systems undergoing PPHP-dependent, PGHS-catalyzed oxidation of (13Z)-RA or RA. These results are consistent with the formation of peroxyl radicals in these systems. In all experiments, the (13Z)-RA isomer appeared to be a better substrate for the enzyme compared to the all-trans isomer. Collectively these results provide further evidence to support the previously proposed mechanism for retinoid oxidation by PGHS involving the intermediacy of C4 carbon

Polyomavirus BK non-coding control region rearrangements in health and disease.

PubMed

Sharma, Preety M; Gupta, Gaurav; Vats, Abhay; Shapiro, Ron; Randhawa, Parmjeet S

2007-08-01

BK virus is an increasingly recognized pathogen in transplanted patients. DNA sequencing of this virus shows considerable genomic variability. To understand the clinical significance of rearrangements in the non-coding control region (NCCR) of BK virus (BKV), we report a meta-analysis of 507 sequences, including 40 sequences generated in our own laboratory, for associations between rearrangements and disease, tissue tropism, geographic origin, and viral genotype. NCCR rearrangements were less frequent in (a) asymptomatic BKV viruria compared to patients viral nephropathy (1.7% vs. 22.5%), and (b) viral genotype 1 compared to other genotypes (2.4% vs. 11.2%). Rearrangements were commoner in malignancy (78.6%), and Norwegians (45.7%), and less common in East Indians (0%), and Japanese (4.3%). A surprising number of rearranged sequences were reported from mononuclear cells of healthy subjects, whereas most plasma sequences were archetypal. This difference could not be related to potential recombinase activity in lymphocytes, as consensus recombination signal sequences could not be found in the NCCR region. NCCR rearrangements are neither required nor a sufficient condition to produce clinical disease. BKV nephropathy and hemorrhagic cystitis are not associated with any unique NCCR configuration or nucleotide sequence.

Structural and stereoelectronic insights into oxygenase-catalyzed formation of ethylene from 2-oxoglutarate.

PubMed

Zhang, Zhihong; Smart, Tristan J; Choi, Hwanho; Hardy, Florence; Lohans, Christopher T; Abboud, Martine I; Richardson, Melodie S W; Paton, Robert S; McDonough, Michael A; Schofield, Christopher J

2017-05-02

Ethylene is important in industry and biological signaling. In plants, ethylene is produced by oxidation of 1-aminocyclopropane-1-carboxylic acid, as catalyzed by 1-aminocyclopropane-1-carboxylic acid oxidase. Bacteria catalyze ethylene production, but via the four-electron oxidation of 2-oxoglutarate to give ethylene in an arginine-dependent reaction. Crystallographic and biochemical studies on the Pseudomonas syringae ethylene-forming enzyme reveal a branched mechanism. In one branch, an apparently typical 2-oxoglutarate oxygenase reaction to give succinate, carbon dioxide, and sometimes pyrroline-5-carboxylate occurs. Alternatively, Grob-type oxidative fragmentation of a 2-oxoglutarate-derived intermediate occurs to give ethylene and carbon dioxide. Crystallographic and quantum chemical studies reveal that fragmentation to give ethylene is promoted by binding of l-arginine in a nonoxidized conformation and of 2-oxoglutarate in an unprecedented high-energy conformation that favors ethylene, relative to succinate formation.

Rhodium-Catalyzed Acyloxy Migration of Propargylic Esters in Cycloadditions, Inspiration from Recent “Gold Rush”

PubMed Central

Shu, Xing-Zhong; Shu, Dongxu; Schienebeck, Casi M.

2012-01-01

Transition metal-catalyzed acyloxy migration of propargylic esters offers versatile entries to allene and vinyl carbene intermediates for various fascinating subsequent transformations. Most π-acidic metals (e.g. gold and platinum) are capable of facilitating these acyloxy migration events. However, very few of these processes involve redox chemistry, which are well-known for most other transition metals such as rhodium. The coupling of acyloxy migration of propargylic esters with oxidative addition, migratory insertion, and reductive elimination may lead to ample new opportunities for the design of new reactions. This tutorial review summarizes recent developments in Rh-catalyzed 1,3- and 1,2-acyloxy migration of propargylic esters in a number of cycloaddition reactions. Related Au- and Pt-catalyzed cycloadditions involving acyloxy migration are also discussed. PMID:22895533

Regioselective Ni-Catalyzed Carboxylation of Allylic and Propargylic Alcohols with Carbon Dioxide.

PubMed

Chen, Yue-Gang; Shuai, Bin; Ma, Cong; Zhang, Xiu-Jie; Fang, Ping; Mei, Tian-Sheng

2017-06-02

An efficient Ni-catalyzed reductive carboxylation of allylic alcohols with CO 2 has been successfully developed, providing linear β,γ-unsaturated carboxylic acids as the sole regioisomer with generally high E/Z stereoselectivity. In addition, the carboxylic acids can be generated from propargylic alcohols via hydrogenation to give allylic alcohol intermediates, followed by carboxylation. A preliminary mechanistic investigation suggests that the hydrogenation step is made possible by a Ni hydride intermediate produced by a hydrogen atom transfer from water.

Heterogeneity of BCR-ABL rearrangement in patients with chronic myeloid leukemia in Pakistan.

PubMed

Tabassum, Najia; Saboor, Mohammad; Ghani, Rubina; Moinuddin, Moinuddin

2014-07-01

Breakpoint cluster region-Abelson (BCR-ABL) rearrangement or Philadelphia (Ph) chromosome in Chronic Myeloid Leukemia (CML) is derived from a reciprocal chromosomal translocation between ABL gene on chromosome 9 and BCR gene on chromosome 22. This chimeric protein has various sizes and therefore different clinical behaviour. The purpose of this study was to determine the heterogeneity of BCR-ABL rearrangement in patients with Ph(+)CML in Pakistan. The study was conducted at Civil Hospital and Baqai Institute of Hematology (BIH) Karachi. Blood samples from 25 patients with CML were collected. Multiplex reverse transcription polymerase chain reaction (RT-PCR) was performed to identify various BCR-ABL transcripts. All 25 samples showed BCR-ABL rearrangements. Out of these, 24 (96%) patients expressed p210 BCR-ABL rearrangements i.e. 60% (n=15) had b3a2 and 32% (n=8) had b2a2 rearrangements. Co-expression of b3a2 /b2a2 rearrangement and p190 (e1a3) rearrangement was also identified in two patients. It is apparent that majority of the patients had p210 BCR-ABL rearrangements. Frequency of co-expression and rare fusion transcripts was very low.

A FMO-controlled reaction path in the benzil-benzilic acid rearrangement.

PubMed

Yamabe, Shinichi; Tsuchida, Noriko; Yamazaki, Shoko

2006-03-03

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.

The potential of clofarabine in MLL-rearranged infant acute lymphoblastic leukaemia.

PubMed

Stumpel, Dominique J P M; Schneider, Pauline; Pieters, Rob; Stam, Ronald W

2015-09-01

MLL-rearranged acute lymphoblastic leukaemia (ALL) in infants is the most difficult-to-treat type of childhood ALL, displaying a chemotherapy-resistant phenotype, and unique histone modifications, gene expression signatures and DNA methylation patterns. MLL-rearranged infant ALL responds remarkably well to nucleoside analogue drugs in vitro, such as cytarabine and cladribine, and to the demethylating agents decitabine and zebularine as measured by cytotoxicity assays. These observations led to the inclusion of cytarabine into the treatment regimens currently used for infants with ALL. However, survival chances for infants with MLL-rearranged ALL do still not exceed 30-40%. Here we explored the in vitro potential of the novel nucleoside analogue clofarabine for MLL-rearranged infant ALL. Therefore we used both cell line models as well as primary patient cells. Compared with other nucleoside analogues, clofarabine effectively targeted primary MLL-rearranged infant ALL cells at the lowest concentrations, with median LC50 values of ∼25 nM. Interestingly, clofarabine displayed synergistic cytotoxic effects in combination with cytarabine. Furthermore, at concentrations of 5-10nM clofarabine induced demethylation of the promoter region of the tumour suppressor gene FHIT (Fragile Histidine Triad), a gene typically hypermethylated in MLL-rearranged ALL. Demethylation of the FHIT promoter region was accompanied by subtle re-expression of this gene both at the mRNA and protein level. We conclude that clofarabine is an interesting candidate for further studies in MLL-rearranged ALL in infants. Copyright © 2015 Elsevier Ltd. All rights reserved.

Detecting Gene Rearrangements in Patient Populations Through a 2-Step Diagnostic Test Comprised of Rapid IHC Enrichment Followed by Sensitive Next-Generation Sequencing

PubMed Central

Murphy, Danielle A.; Ely, Heather A.; Shoemaker, Robert; Boomer, Aaron; Culver, Brady P.; Hoskins, Ian; Haimes, Josh D.; Walters, Ryan D.; Fernandez, Diane; Stahl, Joshua A.; Lee, Jeeyun; Kim, Kyoung-Mee; Lamoureux, Jennifer

2017-01-01

Targeted therapy combined with companion diagnostics has led to the advancement of next-generation sequencing (NGS) for detection of molecular alterations. However, using a diagnostic test to identify patient populations with low prevalence molecular alterations, such as gene rearrangements, poses efficiency, and cost challenges. To address this, we have developed a 2-step diagnostic test to identify NTRK1, NTRK2, NTRK3, ROS1, and ALK rearrangements in formalin-fixed paraffin-embedded clinical specimens. This test is comprised of immunohistochemistry screening using a pan-receptor tyrosine kinase cocktail of antibodies to identify samples expressing TrkA (encoded by NTRK1), TrkB (encoded by NTRK2), TrkC (encoded by NTRK3), ROS1, and ALK followed by an RNA-based anchored multiplex polymerase chain reaction NGS assay. We demonstrate that the NGS assay is accurate and reproducible in identification of gene rearrangements. Furthermore, implementation of an RNA quality control metric to assess the presence of amplifiable nucleic acid input material enables a measure of confidence when an NGS result is negative for gene rearrangements. Finally, we demonstrate that performing a pan-receptor tyrosine kinase immunohistochemistry staining enriches detection of the patient population for gene rearrangements from 4% to 9% and has a 100% negative predictive value. Together, this 2-step assay is an efficient method for detection of gene rearrangements in both clinical testing and studies of archival formalin-fixed paraffin-embedded specimens. PMID:27028240

N-triflylthiophosphoramide catalyzed enantioselective Mukaiyama aldol reaction of aldehydes with silyl enol ethers of ketones.

PubMed

Cheon, Cheol Hong; Yamamoto, Hisashi

2010-06-04

The first Brønsted acid catalyzed asymmetric Mukaiyama aldol reaction of aldehydes using silyl enol ethers of ketones as nucleophiles has been reported. A variety of aldehydes and silyl enol ethers of ketones afforded the aldol products in excellent yields and good to excellent enantioselectivities. Mechanistic studies revealed that the actual catalyst may be changed from the silylated Brønsted acid to the Brønsted acid itself depending on the reaction temperature.

Chromosome rearrangements and the evolution of genome structuring and adaptability.

PubMed

Crombach, Anton; Hogeweg, Paulien

2007-05-01

Eukaryotes appear to evolve by micro and macro rearrangements. This is observed not only for long-term evolutionary adaptation, but also in short-term experimental evolution of yeast, Saccharomyces cerevisiae. Moreover, based on these and other experiments it has been postulated that repeat elements, retroposons for example, mediate such events. We study an evolutionary model in which genomes with retroposons and a breaking/repair mechanism are subjected to a changing environment. We show that retroposon-mediated rearrangements can be a beneficial mutational operator for short-term adaptations to a new environment. But simply having the ability of rearranging chromosomes does not imply an advantage over genomes in which only single-gene insertions and deletions occur. Instead, a structuring of the genome is needed: genes that need to be amplified (or deleted) in a new environment have to cluster. We show that genomes hosting retroposons, starting with a random order of genes, will in the long run become organized, which enables (fast) rearrangement-based adaptations to the environment. In other words, our model provides a "proof of principle" that genomes can structure themselves in order to increase the beneficial effect of chromosome rearrangements.

Chromosome Rearrangements That Involve the Nucleolus Organizer Region in Neurospora

PubMed Central

Perkins, D. D.; Raju, N. B.; Barry, E. G.; Butler, D. K.

1995-01-01

In ~3% of Neurospora crassa rearrangements, part of a chromosome arm becomes attached to the nucleolus organizer region (NOR) at one end of chromosome 2 (linkage group V). Investigations with one inversion and nine translocations of this type are reported here. They appear genetically to be nonreciprocal and terminal. When a rearrangement is heterozygous, about one-third of viable progeny are segmental aneuploids with the translocated segment present in two copies, one in normal position and one associated with the NOR. Duplications from many of the rearrangements are highly unstable, breaking down by loss of the NOR-attached segment to restore normal chromosome sequence. When most of the rearrangements are homozygous, attenuated strands can be seen extending through the unstained nucleolus at pachytene, joining the translocated distal segment to the remainder of chromosome 2. Although the rearrangements appear genetically to be nonreciprocal, molecular evidence shows that at least several of them are physically reciprocal, with a block of rDNA repeats translocated away from the NOR. Evidence that NOR-associated breakpoints are nonterminal is also provided by intercrosses between pairs of translocations that transfer different-length segments of the same donor-chromosome arm to the NOR. PMID:8582636

Myeloperoxidase-catalyzed incorporation of amines into proteins: role of hypochlorous acid and dichloramines.

PubMed

Thomas, E L; Jefferson, M M; Grisham, M B

1982-11-23

Myeloperoxidase-catalyzed oxidation of chloride (Cl-) to hypochlorous acid (HOCl) resulted in formation of mono- and dichloramine derivatives (RNHCl and RNCl2) of primary amines. The RNCl2 derivatives could undergo a reaction that resulted in incorporation of the R moiety into proteins. The probable mechanism was attack of RNCl2 or an intermediate formed in the decomposition of RNCl2 on histidine, tyrosine, and cystine residues and on lysine residues at high pH. Incorporation of radioactivity from labeled amines into stable, high molecular weight derivatives of proteins was measured by acid or acetone precipitation and by gel chromatography and electrophoresis. Whereas formation of RNCl2 was favored at low pH, the subsequent incorporation reaction was favored at high pH. Up to several hours were required for the maximum amount of incorporation, which was less than 10% of the label in RNCl2. For the amines tested, incorporation was in the order histamine greater than 1,2-diaminoethane greater than putrescine greater than taurine greater than lysine greater than glucosamine greater than leucine greater than methylamine. Initiation of the reaction required HOCl, and oxidized forms of bromide, iodide, or thiocyanate did not substitute. Inhibitors of incorporation fell into three classes. First, ammonia or amines competed with the labeled amine for reaction with HOCl, so that larger amounts of HOCl were required. Second, readily oxidized substances such as sulfhydryl or diketo compounds or thioethers (methionine) reduced RNCl2. Third, certain compounds competed with protein as the acceptor for the incorporation reaction. The amount required to block incorporation into protein depended on protein concentration. Among these inhibitors were imidazole compounds (histidine), phenols (tyrosine), and disulfides (glutathione disulfide, GSSG). Low yields of derivatives of histidine, tyrosine, and GSSG were detected by thin-layer chromatography. Acid-precipitable derivatives were

Tissue cohesion and the mechanics of cell rearrangement.

PubMed

David, Robert; Luu, Olivia; Damm, Erich W; Wen, Jason W H; Nagel, Martina; Winklbauer, Rudolf

2014-10-01

Morphogenetic processes often involve the rapid rearrangement of cells held together by mutual adhesion. The dynamic nature of this adhesion endows tissues with liquid-like properties, such that large-scale shape changes appear as tissue flows. Generally, the resistance to flow (tissue viscosity) is expected to depend on the cohesion of a tissue (how strongly its cells adhere to each other), but the exact relationship between these parameters is not known. Here, we analyse the link between cohesion and viscosity to uncover basic mechanical principles of cell rearrangement. We show that for vertebrate and invertebrate tissues, viscosity varies in proportion to cohesion over a 200-fold range of values. We demonstrate that this proportionality is predicted by a cell-based model of tissue viscosity. To do so, we analyse cell adhesion in Xenopus embryonic tissues and determine a number of parameters, including tissue surface tension (as a measure of cohesion), cell contact fluctuation and cortical tension. In the tissues studied, the ratio of surface tension to viscosity, which has the dimension of a velocity, is 1.8 µm/min. This characteristic velocity reflects the rate of cell-cell boundary contraction during rearrangement, and sets a limit to rearrangement rates. Moreover, we propose that, in these tissues, cell movement is maximally efficient. Our approach to cell rearrangement mechanics links adhesion to the resistance of a tissue to plastic deformation, identifies the characteristic velocity of the process, and provides a basis for the comparison of tissues with mechanical properties that may vary by orders of magnitude. © 2014. Published by The Company of Biologists Ltd.

Deep cytoplasmic rearrangements in ventralized Xenopus embryos

NASA Technical Reports Server (NTRS)

Brown, E. E.; Denegre, J. M.; Danilchik, M. V.

1993-01-01

Following fertilization in Xenopus, dramatic rearrangements of the egg cytoplasm relocalize maternally synthesized egg components. During the first cell cycle the vegetal yolk mass rotates relative to the egg surface, toward the sperm entry point (SEP) (J. P. Vincent, G. F. Oster, and J. C. Gerhart, 1986, Dev. Biol. 113, 484-500), while concomitant deep cytoplasmic rearrangements occur in the animal hemisphere (M. V. Danilchik and J. M. Denegre, 1991, Development 111, 845-856). In this paper we examine the role of vegetal yolk mass rotation in producing the animal cytoplasmic rearrangements. We inhibited rotation by uv-irradiating embryos during the first cell cycle, a treatment that yields an extremely ventralized phenotype. Both uv-irradiated embryos and unirradiated control embryos show cytoplasmic rearrangements in the animal hemisphere during the first cell cycle. Cytoplasmic rearrangements on the SEP side of the embryo associated with the path of the sperm pronucleus, plus a swirl on the anti-SEP (dorsal) side, are seen, whether or not yolk mass rotation has occurred. This result suggests a role for the expanding sperm aster in directing animal hemisphere cytoplasmic movements. In unirradiated control embryos the anti-SEP (dorsal) swirl is larger than that in uv-irradiated embryos and often extends into the vegetal hemisphere, consistent with the animal cytoplasm having been pulled dorsally and vegetally by the sliding vegetal yolk mass. Thus the yolk mass rotation may normally enhance the dorsalward cytoplasmic movement, begun by the sperm aster, enough to induce normal axis formation. We extended our observations of unirradiated control and uv-irradiated embryos through early cleavages. The vegetal extent of the anti-SEP (dorsal) swirl pattern seen in control embryos persists through the early cleavage period, such that labeled animal cytoplasm extends deep into dorsal third-tier blastomeres at the 32-cell stage. Significantly, in uv-irradiated embryos

Dynamics of Genome Rearrangement in Bacterial Populations

PubMed Central

Darling, Aaron E.; Miklós, István; Ragan, Mark A.

2008-01-01

Genome structure variation has profound impacts on phenotype in organisms ranging from microbes to humans, yet little is known about how natural selection acts on genome arrangement. Pathogenic bacteria such as Yersinia pestis, which causes bubonic and pneumonic plague, often exhibit a high degree of genomic rearrangement. The recent availability of several Yersinia genomes offers an unprecedented opportunity to study the evolution of genome structure and arrangement. We introduce a set of statistical methods to study patterns of rearrangement in circular chromosomes and apply them to the Yersinia. We constructed a multiple alignment of eight Yersinia genomes using Mauve software to identify 78 conserved segments that are internally free from genome rearrangement. Based on the alignment, we applied Bayesian statistical methods to infer the phylogenetic inversion history of Yersinia. The sampling of genome arrangement reconstructions contains seven parsimonious tree topologies, each having different histories of 79 inversions. Topologies with a greater number of inversions also exist, but were sampled less frequently. The inversion phylogenies agree with results suggested by SNP patterns. We then analyzed reconstructed inversion histories to identify patterns of rearrangement. We confirm an over-representation of “symmetric inversions”—inversions with endpoints that are equally distant from the origin of chromosomal replication. Ancestral genome arrangements demonstrate moderate preference for replichore balance in Yersinia. We found that all inversions are shorter than expected under a neutral model, whereas inversions acting within a single replichore are much shorter than expected. We also found evidence for a canonical configuration of the origin and terminus of replication. Finally, breakpoint reuse analysis reveals that inversions with endpoints proximal to the origin of DNA replication are nearly three times more frequent. Our findings represent the

Telomerase activation by genomic rearrangements in high-risk neuroblastoma

PubMed Central

Peifer, Martin; Hertwig, Falk; Roels, Frederik; Dreidax, Daniel; Gartlgruber, Moritz; Menon, Roopika; Krämer, Andrea; Roncaioli, Justin L.; Sand, Frederik; Heuckmann, Johannes M.; Ikram, Fakhera; Schmidt, Rene; Ackermann, Sandra; Engesser, Anne; Kahlert, Yvonne; Vogel, Wenzel; Altmüller, Janine; Nürnberg, Peter; Thierry-Mieg, Jean; Thierry-Mieg, Danielle; Mariappan, Aruljothi; Heynck, Stefanie; Mariotti, Erika; Henrich, Kai-Oliver; Glöckner, Christian; Bosco, Graziella; Leuschner, Ivo; Schweiger, Michal R.; Savelyeva, Larissa; Watkins, Simon C.; Shao, Chunxuan; Bell, Emma; Höfer, Thomas; Achter, Viktor; Lang, Ulrich; Theissen, Jessica; Volland, Ruth; Saadati, Maral; Eggert, Angelika; de Wilde, Bram; Berthold, Frank; Peng, Zhiyu; Zhao, Chen; Shi, Leming; Ortmann, Monika; Büttner, Reinhard; Perner, Sven; Hero, Barbara; Schramm, Alexander; Schulte, Johannes H.; Herrmann, Carl; O’Sullivan, Roderick J.; Westermann, Frank; Thomas, Roman K.; Fischer, Matthias

2016-01-01

Neuroblastoma is a malignant paediatric tumour of the sympathetic nervous system1. Roughly half of these tumours regress spontaneously or are cured by limited therapy. By contrast, high-risk neuroblastomas have an unfavourable clinical course despite intensive multimodal treatment, and their molecular basis has remained largely elusive2–4. Here we have performed whole-genome sequencing of 56 neuroblastomas (high-risk, n = 39; low-risk, n = 17) and discovered recurrent genomic rearrangements affecting a chromosomal region at 5p15.33 proximal of the telomerase reverse transcriptase gene (TERT). These rearrangements occurred only in high-risk neuroblastomas (12/39, 31%) in a mutually exclusive fashion with MYCN amplifications and ATRX mutations, which are known genetic events in this tumour type1,2,5. In an extended case series (n = 217), TERT rearrangements defined a subgroup of high-risk tumours with particularly poor outcome. Despite a large structural diversity of these rearrangements, they all induced massive transcriptional upregulation of TERT. In the remaining high-risk tumours, TERT expression was also elevated in MYCN-amplified tumours, whereas alternative lengthening of telomeres was present in neuroblastomas without TERT or MYCN alterations, suggesting that telomere lengthening represents a central mechanism defining this subtype. The 5p15.33 rearrangements juxtapose the TERT coding sequence to strong enhancer elements, resulting in massive chromatin remodelling and DNA methylation of the affected region. Supporting a functional role of TERT, neuroblastoma cell lines bearing rearrangements or amplified MYCN exhibited both upregulated TERT expression and enzymatic telomerase activity. In summary, our findings show that remodelling of the genomic context abrogates transcriptional silencing of TERT in high-risk neuroblastoma and places telomerase activation in the centre of transformation in a large fraction of these tumours. PMID:26466568

Record of drainage rearrangement and erosion in a transpressive orogen: relative role of horizontal and vertical rock advection in drainage evolution

NASA Astrophysics Data System (ADS)

Brocard, G. Y.; Teyssier, C.; Dunlap, W. J.; Willenbring, J.; Simon-Labric, T.; Authemayou, C.

2008-12-01

, geochemical analyses, Ar40 -Ar39 dating of volcanic tuffs, 10 Be-26 Al burial dating, and apatite He cooling ages of the bedrock. Coupled analyses of erosion and drainage rearrangement show that, in the studied case, catchment growth occurred over 107 years. Most of the catchment erosion and growth is attributable to uplift along the PF rather than strike-slip motion, although both motion types contribute to the rearrangement. Growth of the catchment is strongly catalyzed by a wealth of other factors, such as river avulsion, volcanism, karstic flow, phreatic flow, and aridity resulting from catchment deepening.

Pyranoside-into-furanoside rearrangement: new reaction in carbohydrate chemistry and its application in oligosaccharide synthesis.

PubMed

Krylov, Vadim B; Argunov, Dmitry A; Vinnitskiy, Dmitry Z; Verkhnyatskaya, Stella A; Gerbst, Alexey G; Ustyuzhanina, Nadezhda E; Dmitrenok, Andrey S; Huebner, Johannes; Holst, Otto; Siebert, Hans-Christian; Nifantiev, Nikolay E

2014-12-08

Great interest in natural furanoside-containing compounds has challenged the development of preparative methods for their synthesis. Herein a novel reaction in carbohydrate chemistry, namely a pyranoside-into-furanoside (PIF) rearrangement permitting the transformation of selectively O-substituted pyranosides into the corresponding furanosides is reported. The discovered process includes acid-promoted sulfation accompanied by rearrangement of the pyranoside ring into a furanoside ring followed by solvolytic O-desulfation. This process, which has no analogy in organic chemistry, was shown to be a very useful tool for the synthesis of furanoside-containing complex oligosaccharides, which was demonstrated by synthesizing disaccharide derivatives α-D-Galp-(1→3)-β-D-Galf-OPr, 3-O-s-lactyl-β-D-Galf-(1→3)-β-D-Glcp-OPr, and α-L-Fucf-(1→4)-β-D-GlcpA-OPr related to polysaccharides from the bacteria Klebsiella pneumoniae and Enterococcus faecalis and the brown seaweed Chordaria flagelliformis. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Sonochemical enzyme-catalyzed regioselective acylation of flavonoid glycosides.

PubMed

Ziaullah; Rupasinghe, H P Vasantha

2016-04-01

This work compares a highly efficient and alternative method of sonication-assisted lipase catalyzed acylation of quercetin-3-O-glucoside and phloretin-2'-glucoside, using Candida antarctica lipase B (Novozyme 435(®)), with a range of fatty acids. In this study, sonication-assisted irradiation coupled with stirring has been found to be more efficient and economical than conventional reaction conditions. Sonication-assisted acylation accelerated the reactions and reduced the time required by 4-5 folds. Copyright © 2016 Elsevier Inc. All rights reserved.

Pyruvate Decarboxylase Catalyzes Decarboxylation of Branched-Chain 2-Oxo Acids but Is Not Essential for Fusel Alcohol Production by Saccharomyces cerevisiae

PubMed Central

ter Schure, Eelko G.; Flikweert, Marcel T.; van Dijken, Johannes P.; Pronk, Jack T.; Verrips, C. Theo

1998-01-01

The fusel alcohols 3-methyl-1-butanol, 2-methyl-1-butanol, and 2-methyl-propanol are important flavor compounds in yeast-derived food products and beverages. The formation of these compounds from branched-chain amino acids is generally assumed to occur via the Ehrlich pathway, which involves the concerted action of a branched-chain transaminase, a decarboxylase, and an alcohol dehydrogenase. Partially purified preparations of pyruvate decarboxylase (EC 4.1.1.1) have been reported to catalyze the decarboxylation of the branched-chain 2-oxo acids formed upon transamination of leucine, isoleucine, and valine. Indeed, in a coupled enzymatic assay with horse liver alcohol dehydrogenase, cell extracts of a wild-type Saccharomyces cerevisiae strain exhibited significant decarboxylation rates with these branched-chain 2-oxo acids. Decarboxylation of branched-chain 2-oxo acids was not detectable in cell extracts of an isogenic strain in which all three PDC genes had been disrupted. Experiments with cell extracts from S. cerevisiae mutants expressing a single PDC gene demonstrated that both PDC1- and PDC5-encoded isoenzymes can decarboxylate branched-chain 2-oxo acids. To investigate whether pyruvate decarboxylase is essential for fusel alcohol production by whole cells, wild-type S. cerevisiae and an isogenic pyruvate decarboxylase-negative strain were grown on ethanol with a mixture of leucine, isoleucine, and valine as the nitrogen source. Surprisingly, the three corresponding fusel alcohols were produced in both strains. This result proves that decarboxylation of branched-chain 2-oxo acids via pyruvate decarboxylase is not an essential step in fusel alcohol production. PMID:9546164

Chromosome rearrangements via template switching between diverged repeated sequences

PubMed Central

Anand, Ranjith P.; Tsaponina, Olga; Greenwell, Patricia W.; Lee, Cheng-Sheng; Du, Wei; Petes, Thomas D.

2014-01-01

Recent high-resolution genome analyses of cancer and other diseases have revealed the occurrence of microhomology-mediated chromosome rearrangements and copy number changes. Although some of these rearrangements appear to involve nonhomologous end-joining, many must have involved mechanisms requiring new DNA synthesis. Models such as microhomology-mediated break-induced replication (MM-BIR) have been invoked to explain these rearrangements. We examined BIR and template switching between highly diverged sequences in Saccharomyces cerevisiae, induced during repair of a site-specific double-strand break (DSB). Our data show that such template switches are robust mechanisms that give rise to complex rearrangements. Template switches between highly divergent sequences appear to be mechanistically distinct from the initial strand invasions that establish BIR. In particular, such jumps are less constrained by sequence divergence and exhibit a different pattern of microhomology junctions. BIR traversing repeated DNA sequences frequently results in complex translocations analogous to those seen in mammalian cells. These results suggest that template switching among repeated genes is a potent driver of genome instability and evolution. PMID:25367035

The first characterization of free radicals formed from cellular COX-catalyzed peroxidation.

PubMed

Gu, Yan; Xu, Yi; Law, Benedict; Qian, Steven Y

2013-04-01

Through free radical-mediated peroxidation, cyclooxygenase (COX) can metabolize dihomo-γ-linolenic acid (DGLA) and arachidonic acid (AA) to form well-known bioactive metabolites, namely, the 1-series of prostaglandins (PGs1) and the 2-series of prostaglandins (PGs2), respectively. Unlike PGs2, which are generally viewed as proinflammatory and procarcinogenic PGs, PGs1 may possess anti-inflammatory and anti-cancer activity. Previous studies using ovine COX along with spin trapping and the LC/ESR/MS technique have shown that certain exclusive free radicals are generated from different free radical reactions in DGLA and AA peroxidation. However, it has been unclear whether the differences were associated with the contrasting bioactivity of DGLA vs AA. The aim of this study was to refine the LC/MS and spin trapping technique to make it possible for the association between free radicals and cancer cell growth to be directly tested. Using a colon cancer cell line, HCA-7 colony 29, and LC/MS along with a solid-phase extraction, we were able to characterize the reduced forms of radical adducts (hydroxylamines) as the free radicals generated from cellular COX-catalyzed peroxidation. For the first time, free radicals formed in the COX-catalyzed peroxidation of AA vs DGLA and their association with cancer cell growth were assessed (cell proliferation via MTS and cell cycle distribution via propidium iodide staining) in the same experimental setting. The exclusive free radicals formed from the COX-catalyzed peroxidation of AA and DGLA were shown to be correlated with the cell growth response. Our results indicate that free radicals generated from the distinct radical reactions in COX-catalyzed peroxidation may represent the novel metabolites of AA and DGLA that correspond to their contrasting bioactivity. Copyright © 2012 Elsevier Inc. All rights reserved.

The First Characterization of Free Radicals Formed From Cellular COX-Catalyzed Peroxidation

PubMed Central

Gu, Yan; Xu, Yi; Law, Benedict; Qian, Steven Y.

2014-01-01

Through free radical-mediated peroxidation, cyclooxygenase (COX) can metabolize dihomo-γ-linolenic acid (DGLA) and arachidonic acid(AA) to form well-known bioactive metabolites, namely, the 1-series of prostaglandins (PGs1) and 2-series of prostaglandins(PGs2), respectively. Unlike PGs2, which are generally viewed as pro-inflammatory and pro-carcinogenic PGs, PGs1 may possess anti-inflammatory and anti-cancer activity. Previous studies using ovine COX along with spin trapping and the LC/ESR/MS technique have shown that certain exclusive free radicals are generated from different free radical reactions in DGLA and AA peroxidation. However, it has been unclear whether the differences were associated with the contrasting bioactivity of DGLA vs. AA. The aim of this study was to refine the LC/MS and spin-trapping technique to make it possible for the association between free radicals and cancer cell growth to be directly tested. Using a colon cancer cell line, HCA-7 colony 29, and LC/MS along with a solid phase extraction, we were able to characterize the reduced forms of radical adducts (hydroxylamines) as the free radicals generated from cellular COX-catalyzed peroxidation. For the first time, free radicals formed in the COX-catalyzed peroxidation of AA vs. DGLA and their association with cancer cell growth was assessed (cell proliferation via MTS and cell cycle distribution via PI staining) in the same experimental setting. The exclusive free radicals formed from the COX-catalyzed peroxidation of AA and DGLA were shown to be correlated with the cell growth response. Our results indicate that free radicals generated from the distinct radical reactions in COX-catalyzed peroxidation may represent the novel metabolites of AA and DGLA that correspond to their contrasting bioactivity. PMID:23261941

Heterogeneity of BCR-ABL rearrangement in patients with chronic myeloid leukemia in Pakistan

PubMed Central

Tabassum, Najia; Saboor, Mohammad; Ghani, Rubina; Moinuddin, Moinuddin

2014-01-01

Background and Objective: Breakpoint cluster region-Abelson (BCR-ABL) rearrangement or Philadelphia (Ph) chromosome in Chronic Myeloid Leukemia (CML) is derived from a reciprocal chromosomal translocation between ABL gene on chromosome 9 and BCR gene on chromosome 22. This chimeric protein has various sizes and therefore different clinical behaviour. The purpose of this study was to determine the heterogeneity of BCR-ABL rearrangement in patients with Ph+CML in Pakistan. Methods: The study was conducted at Civil Hospital and Baqai Institute of Hematology (BIH) Karachi. Blood samples from 25 patients with CML were collected. Multiplex reverse transcription polymerase chain reaction (RT-PCR) was performed to identify various BCR-ABL transcripts. Results: All 25 samples showed BCR-ABL rearrangements. Out of these, 24 (96%) patients expressed p210 BCR-ABL rearrangements i.e. 60% (n=15) had b3a2 and 32% (n=8) had b2a2 rearrangements. Co-expression of b3a2 /b2a2 rearrangement and p190 (e1a3) rearrangement was also identified in two patients. Conclusion: It is apparent that majority of the patients had p210 BCR-ABL rearrangements. Frequency of co-expression and rare fusion transcripts was very low. PMID:25097530

Copper-Catalyzed Oxidative Dehydrogenative Carboxylation of Unactivated Alkanes to Allylic Esters via Alkenes

PubMed Central

2015-01-01

We report copper-catalyzed oxidative dehydrogenative carboxylation (ODC) of unactivated alkanes with various substituted benzoic acids to produce the corresponding allylic esters. Spectroscopic studies (EPR, UV–vis) revealed that the resting state of the catalyst is [(BPI)Cu(O2CPh)] (1-O2CPh), formed from [(BPI)Cu(PPh3)2], oxidant, and benzoic acid. Catalytic and stoichiometric reactions of 1-O2CPh with alkyl radicals and radical probes imply that C–H bond cleavage occurs by a tert-butoxy radical. In addition, the deuterium kinetic isotope effect from reactions of cyclohexane and d12-cyclohexane in separate vessels showed that the turnover-limiting step for the ODC of cyclohexane is C–H bond cleavage. To understand the origin of the difference in products formed from copper-catalyzed amidation and copper-catalyzed ODC, reactions of an alkyl radical with a series of copper–carboxylate, copper–amidate, and copper–imidate complexes were performed. The results of competition experiments revealed that the relative rate of reaction of alkyl radicals with the copper complexes follows the trend Cu(II)–amidate > Cu(II)–imidate > Cu(II)–benzoate. Consistent with this trend, Cu(II)–amidates and Cu(II)–benzoates containing more electron-rich aryl groups on the benzamidate and benzoate react faster with the alkyl radical than do those with more electron-poor aryl groups on these ligands to produce the corresponding products. These data on the ODC of cyclohexane led to preliminary investigation of copper-catalyzed oxidative dehydrogenative amination of cyclohexane to generate a mixture of N-alkyl and N-allylic products. PMID:25389772

Expeditious Preparation of Open-Cage Fullerenes by Rhodium(I)-Catalyzed [2+2+2] Cycloaddition of Diynes and C60: an Experimental and Theoretical Study.

PubMed

Artigas, Albert; Pla-Quintana, Anna; Lledó, Agustí; Roglans, Anna; Solà, Miquel

2018-06-04

A novel methodology to transform C60 into a variety of open-cage fullerene derivatives employing rhodium(I) catalysis has been developed. This transformation encompasses a partially intermolecular [2+2+2] cycloaddition reaction between diynes 1 and C60 to deliver a cyclohexadiene-fused fullerene, which concomitantly undergoes a formal [4+4]/retro-[2+2+2] rearrangement to deliver open-cage fullerenes 2. Most notably, this process occurs without the need of photoexcitation. The complete mechanism of this transformation has been rationalized by DFT calculations, which indicate that, after [2+2+2] cycloaddition, the cyclohexadiene-fused intermediate evolves into the final product through a Rh-catalyzed di-π-methane rearrangement followed by a retro-[2+2+2] cycloaddition. The obtained open-cage fullerenes can be derivatized by Suzuki-Miyaura cross-coupling, or subjected to ring expansion to deliver a 12-membered ring orifice in the fullerene structure. Overall, the methodology presented constitutes a straightforward entry to functional open-cage C60-fullerene derivatives employing catalytic methods. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Initial Reactions in the Biodegradation of 1-Chloro-4-Nitrobenzene by a Newly Isolated Bacterium, Strain LW1

PubMed Central

Katsivela, Eleftheria; Wray, Victor; Pieper, Dietmar H.; Wittich, Rolf-Michael

1999-01-01

Bacterial strain LW1, which belongs to the family Comamonadaceae, utilizes 1-chloro-4-nitrobenzene (1C4NB) as a sole source of carbon, nitrogen, and energy. Suspensions of 1C4NB-grown cells removed 1C4NB from culture fluids, and there was a concomitant release of ammonia and chloride. Under anaerobic conditions LW1 transformed 1C4NB into a product which was identified as 2-amino-5-chlorophenol by 1H and 13C nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry. This transformation indicated that there was partial reduction of the nitro group to the hydroxylamino substituent, followed by Bamberger rearrangement. In the presence of oxygen but in the absence of NAD, fast transformation of 2-amino-5-chlorophenol into a transiently stable yellow product was observed with resting cells and cell extracts. This compound exhibited an absorption maximum at 395 nm and was further converted to a dead-end product with maxima at 226 and 272 nm. The compound formed was subsequently identified by 1H and 13C NMR spectroscopy and mass spectrometry as 5-chloropicolinic acid. In contrast, when NAD was added in the presence of oxygen, only minor amounts of 5-chloropicolinic acid were formed, and a new product, which exhibited an absorption maximum at 306 nm, accumulated. PMID:10103229

Cox-2 inhibitory effects of naturally occurring and modified fatty acids.

PubMed

Ringbom, T; Huss, U; Stenholm , A; Flock, S; Skattebøl, L; Perera, P; Bohlin, L

2001-06-01

In the search for new cyclooxygenase-2 (COX-2) selective inhibitors, the inhibitory effects of naturally occurring fatty acids and some of their structural derivatives on COX-2-catalyzed prostaglandin biosynthesis were investigated. Among these fatty acids, linoleic acid (LA), alpha-linolenic acid (alpha-LNA), myristic acid, and palmitic acid were isolated from a CH(2)Cl(2) extract of the plant Plantago major by bioassay-guided fractionation. Inhibitory effects of other natural, structurally related fatty acids were also investigated: stearic acid, oleic acid, pentadecanoic acid, eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA). Further, the inhibitory effects of these compounds on COX-2- and COX-1-catalyzed prostaglandin biosynthesis was compared with the inhibition of some synthesized analogues of EPA and DHA with ether or thioether functions. The most potent COX-2-catalyzed prostaglandin biosynthesis inhibitor was all-(Z)-5-thia-8,11,14,17-eicosatetraenoic acid (2), followed by EPA, DHA, alpha-LNA, LA, (7E,11Z,14Z,17Z)-5-thiaeicosa-7,11,14,17-tetraenoic acid, all-(Z)-3-thia-6,9,12,15-octadecatetraenoic acid, and (5E,9Z,12Z,15Z,18Z)-3-oxaheneicosa-5,9,12,15,18-pentaenoic acid, with IC(50) values ranging from 3.9 to180 microM. The modified compound 2 and alpha-LNA were most selective toward COX-2, with COX-2/COX-1 ratios of 0.2 and 0.1, respectively. This study shows that several of the natural fatty acids as well as all of the semisynthetic thioether-containing fatty acids inhibited COX-2-catalyzed prostaglandin biosynthesis, where alpha-LNA and compound 2 showed selectivity toward COX-2.

Iron-Catalyzed Enantioselective Cross-Coupling Reactions of α-Chloroesters with Aryl Grignard Reagents.

PubMed

Jin, Masayoshi; Adak, Laksmikanta; Nakamura, Masaharu

2015-06-10

The first iron-catalyzed enantioselective cross-coupling reaction between an organometallic compound and an organic electrophile is reported. Synthetically versatile racemic α-chloro- and α-bromoalkanoates were coupled with aryl Grignard reagents in the presence of catalytic amounts of an iron salt and a chiral bisphosphine ligand, giving the products in high yields with acceptable and synthetically useful enantioselectivities (er up to 91:9). The produced α-arylalkanoates were readily converted to the corresponding α-arylalkanoic acids with high optical enrichment (er up to >99:1) via simple deprotections/recrystallizations. The results of radical probe experiments are consistent with a mechanism that involves the formation of an alkyl radical intermediate, which undergoes subsequent enantioconvergent arylation in an intermolecular manner. The developed asymmetric coupling offers not only facile and practical access to various chiral α-arylalkanoic acid derivatives, which are of significant pharmaceutical importance, but also a basis of controlling enantioselectivity in an iron-catalyzed organometallic transformation.

Spontaneous, Metal-Catalyzed, and Enzyme-Catalyzed Decarboxylation of Oxalosuccinic Acid.

DTIC Science & Technology

1980-01-01

acid, 2,4- dinitrophenylhydrazine was added. This yielded a hydrazone which, after two recrystallizations, melted at 2200C. A sample of the a...accurately determined to be 24,500 at a wavelength of 352 nm (46). 34 2,4- Dinitrophenylhydrazine . Obtained from the Eastman Kodak Chemicals Division...reaction with 2,4- dinitrophenylhydrazine (57). The reaction mixture was sampled hourly during the daytime for a period of three days. The concentration of a

Rhodium enalcarbenoids: direct synthesis of indoles by rhodium(II)-catalyzed [4+2] benzannulation of pyrroles.

PubMed

Dawande, Sudam Ganpat; Kanchupalli, Vinaykumar; Kalepu, Jagadeesh; Chennamsetti, Haribabu; Lad, Bapurao Sudam; Katukojvala, Sreenivas

2014-04-14

Disclosed herein is the design of an unprecedented electrophilic rhodium enalcarbenoid which results from rhodium(II)-catalyzed decomposition of a new class of enaldiazo compounds. The synthetic utility of these enalcarbenoids has been successfully demonstrated in the first transition-metal-catalyzed [4+2] benzannulation of pyrroles, thus leading to substituted indoles. The new benzannulation has been applied to the efficient synthesis of the natural product leiocarpone as well as a potent adipocyte fatty-acid binding protein inhibitor. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Silica, Alumina and Clay Catalyzed Peptide Bond Formation: Enhanced Efficiency of Alumina Catalyst

NASA Astrophysics Data System (ADS)

Bujdák, Juraj; Rode, Bernd M.

1999-10-01

Catalytic efficiencies of clay (hectorite), silica and alumina were tested in peptide bond formation reactions of glycine (Gly), alanine (Ala), proline (Pro), valine (Val) and leucine (Leu). The reactions were performed as drying/wetting (hectorite) and temperature fluctuation (silica and alumina) experiments at 85 °C. The reactivity of amino acids decreased in order Gly > Ala > Pro ~ Val ~ Leu. The highest catalytic efficiency was observed for alumina, the only catalyst producing oligopeptides in all investigated reaction systems. The peptide bond formation on alumina is probably catalyzed by the same sites and via similar reaction mechanisms as some alumina-catalyzed dehydration reactions used in industrial chemistry.

Detection of Gene Rearrangements in Circulating Tumor Cells: Examples of ALK-, ROS1-, RET-Rearrangements in Non-Small-Cell Lung Cancer and ERG-Rearrangements in Prostate Cancer.

PubMed

Catelain, Cyril; Pailler, Emma; Oulhen, Marianne; Faugeroux, Vincent; Pommier, Anne-Laure; Farace, Françoise

2017-01-01

Circulating tumor cells (CTCs) hold promise as biomarkers to aid in patient treatment stratification and disease monitoring. Because the number of cells is a critical parameter for exploiting CTCs for predictive biomarker's detection, we developed a FISH (fluorescent in situ hybridization) method for CTCs enriched on filters (filter-adapted FISH [FA-FISH]) that was optimized for high cell recovery. To increase the feasibility and reliability of the analyses, we combined fluorescent staining and FA-FISH and developed a semi-automated microscopy method for optimal FISH signal identification in filtration-enriched CTCs . Here we present these methods and their use for the detection and characterization of ALK-, ROS1-, RET-rearrangement in CTCs from non-small-cell lung cancer and ERG-rearrangements in CTCs from prostate cancer patients.

N-Triflylthiophosphoramide Catalyzed Enantioselective Mukaiyama Aldol Reaction of Aldehydes with Silyl Enol Ethers of Ketones

PubMed Central

Cheon, Cheol Hong; Yamamoto, Hisashi

2010-01-01

The first Brønsted acid catalyzed asymmetric Mukaiyama aldol reaction of aldehydes using silyl enol ethers of ketones as nucleophiles has been reported. A variety of aldehydes and silyl enol ethers of ketones afforded the aldol products in excellent yields and good to excellent enantioselectivities. Mechanistic studies revealed that the actual catalyst may be changed from the silylated Brønsted acid to Brønsted acid itself depending on the reaction temperature. PMID:20465277

Enantioselective oxidation of racemic lactic acid to D-lactic acid and pyruvic acid by Pseudomonas stutzeri SDM.

PubMed

Gao, Chao; Qiu, Jianhua; Li, Jingchen; Ma, Cuiqing; Tang, Hongzhi; Xu, Ping

2009-03-01

D-lactic acid and pyruvic acid are two important building block intermediates. Production of D-lactic acid and pyruvic acid from racemic lactic acid by biotransformation is economically interesting. Biocatalyst prepared from 9 g dry cell wt l(-1) of Pseudomonas stutzeri SDM could catalyze 45.00 g l(-1)DL-lactic acid into 25.23 g l(-1)D-lactic acid and 19.70 g l(-1) pyruvic acid in 10h. Using a simple ion exchange process, D-lactic acid and pyruvic acid were effectively separated from the biotransformation system. Co-production of d-lactic acid and pyruvic acid by enantioselective oxidation of racemic lactic acid is technically feasible.

Comparing genomes with rearrangements and segmental duplications.

PubMed

Shao, Mingfu; Moret, Bernard M E

2015-06-15

Large-scale evolutionary events such as genomic rearrange.ments and segmental duplications form an important part of the evolution of genomes and are widely studied from both biological and computational perspectives. A basic computational problem is to infer these events in the evolutionary history for given modern genomes, a task for which many algorithms have been proposed under various constraints. Algorithms that can handle both rearrangements and content-modifying events such as duplications and losses remain few and limited in their applicability. We study the comparison of two genomes under a model including general rearrangements (through double-cut-and-join) and segmental duplications. We formulate the comparison as an optimization problem and describe an exact algorithm to solve it by using an integer linear program. We also devise a sufficient condition and an efficient algorithm to identify optimal substructures, which can simplify the problem while preserving optimality. Using the optimal substructures with the integer linear program (ILP) formulation yields a practical and exact algorithm to solve the problem. We then apply our algorithm to assign in-paralogs and orthologs (a necessary step in handling duplications) and compare its performance with that of the state-of-the-art method MSOAR, using both simulations and real data. On simulated datasets, our method outperforms MSOAR by a significant margin, and on five well-annotated species, MSOAR achieves high accuracy, yet our method performs slightly better on each of the 10 pairwise comparisons. http://lcbb.epfl.ch/softwares/coser. © The Author 2015. Published by Oxford University Press.

A comprehensive molecular cytogenetic analysis of chromosome rearrangements in gibbons

PubMed Central

Capozzi, Oronzo; Carbone, Lucia; Stanyon, Roscoe R.; Marra, Annamaria; Yang, Fengtang; Whelan, Christopher W.; de Jong, Pieter J.; Rocchi, Mariano; Archidiacono, Nicoletta

2012-01-01

Chromosome rearrangements in small apes are up to 20 times more frequent than in most mammals. Because of their complexity, the full extent of chromosome evolution in these hominoids is not yet fully documented. However, previous work with array painting, BAC-FISH, and selective sequencing in two of the four karyomorphs has shown that high-resolution methods can precisely define chromosome breakpoints and map the complex flow of evolutionary chromosome rearrangements. Here we use these tools to precisely define the rearrangements that have occurred in the remaining two karyomorphs, genera Symphalangus (2n = 50) and Hoolock (2n = 38). This research provides the most comprehensive insight into the evolutionary origins of chromosome rearrangements involved in transforming small apes genome. Bioinformatics analyses of the human–gibbon synteny breakpoints revealed association with transposable elements and segmental duplications, providing some insight into the mechanisms that might have promoted rearrangements in small apes. In the near future, the comparison of gibbon genome sequences will provide novel insights to test hypotheses concerning the mechanisms of chromosome evolution. The precise definition of synteny block boundaries and orientation, chromosomal fusions, and centromere repositioning events presented here will facilitate genome sequence assembly for these close relatives of humans. PMID:22892276

Synthesis of ω-Oxo Amino Acids and trans-5-Substituted Proline Derivatives Using Cross-Metathesis of Unsaturated Amino Acids.

PubMed

Salih, Nabaz; Adams, Harry; Jackson, Richard F W

2016-09-16

A range of 7-oxo, 8-oxo, and 9-oxo amino acids, analogues of 8-oxo-2-aminodecanoic acid, one of the key components of the cyclic tetrapeptide apicidin, have been prepared by a three-step process involving copper-catalyzed allylation of serine-, aspartic acid-, and glutamic acid-derived organozinc reagents, followed by cross-metathesis of the resulting terminal alkenes with unsaturated ketones and hydrogenation. The intermediate 7-oxo-5-enones underwent a highly diastereoselective (dr ≥96:4) acid-catalyzed aza-Michael reaction to give trans-2,5-disubstituted pyrrolidines, 5-substituted proline derivatives. The aza-Michael reaction was first observed when the starting enones were allowed to stand in solution in deuterochloroform but can be efficiently promoted by catalytic amounts of dry HCl.

Tyrosine kinase gene rearrangements in epithelial malignancies

PubMed Central

Shaw, Alice T.; Hsu, Peggy P.; Awad, Mark M.; Engelman, Jeffrey A.

2014-01-01

Chromosomal rearrangements that lead to oncogenic kinase activation are observed in many epithelial cancers. These cancers express activated fusion kinases that drive the initiation and progression of malignancy, and often have a considerable response to small-molecule kinase inhibitors, which validates these fusion kinases as ‘druggable’ targets. In this Review, we examine the aetiologic, pathogenic and clinical features that are associated with cancers harbouring oncogenic fusion kinases, including anaplastic lymphoma kinase (ALK), ROS1 and RET. We discuss the clinical outcomes with targeted therapies and explore strategies to discover additional kinases that are activated by chromosomal rearrangements in solid tumours. PMID:24132104

Chemistry of the 1,2-Dioxetane Ring System. Chemiluminescence, Fragmentations, and Catalyzed Rearrangements.

DTIC Science & Technology

1978-04-18

experimental techniques and for an historical perspective on the chemistry of l,2—dioxetanes. Synthesis and Structure of l,2—Dioxetanes There are at...is relatively electron rich and does not contain abstractable allylic hydrogen atoms . The advantage of the photooxidation , of course , is the...however , is that the phenol is acting as an acid causing the rapid dark path reaction of the dioxetane and hence giving rise to an ap- parent large

Palladium- and Copper-Catalyzed Arylation of Carbon-Hydrogen Bonds

PubMed Central

Daugulis, Olafs; Do, Hien-Quang; Shabashov, Dmitry

2010-01-01

The transition-metal-catalyzed functionalization of C-H bonds is a powerful method for generating carbon-carbon bonds. Although significant advances to this field have been reported during the last decade, many challenges remain. First, most of the methods are substrate-specific and thus cannot be generalized. Second, conversions of unactivated (i.e. not benzylic or alpha to heteroatom) sp3 C–H bonds to C–C bonds are rare, with most examples limited to t-butyl groups—a conversion that is inherently simple because there are no β-hydrogens that can be eliminated. Finally, the palladium, rhodium, and ruthenium catalysts routinely used for the conversion of C–H bonds to C–C bonds are expensive. Catalytically active metals that are cheaper and less exotic (e.g. copper, iron, and manganese) are rarely used. This Account describes our attempts to provide solutions to these three problems. We have developed a general method for directing-group-containing arene arylation by aryl iodides. Using palladium acetate as the catalyst, we arylated anilides, benzamides, benzoic acids, benzylamines, and 2-substituted pyridine derivatives under nearly identical conditions. We have also developed a method for the palladium-catalyzed auxiliary-assisted arylation of unactivated sp3 C–H bonds. This procedure allows for the β-arylation of carboxylic acid derivatives and the γ-arylation of amine derivatives. Furthermore, copper catalysis can be used to mediate the arylation of acidic arene C–H bonds (i.e. those with pKa values <35 in DMSO). Using a copper iodide catalyst in combination with a base and a phenanthroline ligand, we successfully arylated electron-rich and electron-deficient heterocycles and electron-poor arenes possessing at least two electron-withdrawing groups. The reaction exhibits unusual regioselectivity: arylation occurs at the most hindered position. This copper-catalyzed method supplements the well-known C–H activation/borylation methodology, in which

Palladium- and copper-catalyzed arylation of carbon-hydrogen bonds.

PubMed

Daugulis, Olafs; Do, Hien-Quang; Shabashov, Dmitry

2009-08-18

The transition-metal-catalyzed functionalization of C-H bonds is a powerful method for generating carbon-carbon bonds. Although significant advances to this field have been reported during the past decade, many challenges remain. First, most of the methods are substrate-specific and thus cannot be generalized. Second, conversions of unactivated (i.e., not benzylic or alpha to heteroatom) sp(3) C-H bonds to C-C bonds are rare, with most examples limited to t-butyl groups, a conversion that is inherently simple because there are no beta-hydrogens that can be eliminated. Finally, the palladium, rhodium, and ruthenium catalysts routinely used for the conversion of C-H bonds to C-C bonds are expensive. Catalytically active metals that are cheaper and less exotic (e.g., copper, iron, and manganese) are rarely used. This Account describes our attempts to provide solutions to these three problems. We have developed a general method for directing-group-containing arene arylation by aryl iodides. Using palladium acetate as the catalyst, we arylated anilides, benzamides, benzoic acids, benzylamines, and 2-substituted pyridine derivatives under nearly identical conditions. We have also developed a method for the palladium-catalyzed auxiliary-assisted arylation of unactivated sp(3) C-H bonds. This procedure allows for the beta-arylation of carboxylic acid derivatives and the gamma-arylation of amine derivatives. Furthermore, copper catalysis can be used to mediate the arylation of acidic arene C-H bonds (i.e., those with pK(a) values <35 in DMSO). Using a copper iodide catalyst in combination with a base and a phenanthroline ligand, we successfully arylated electron-rich and electron-deficient heterocycles and electron-poor arenes possessing at least two electron-withdrawing groups. The reaction exhibits unusual regioselectivity: arylation occurs at the most hindered position. This copper-catalyzed method supplements the well-known C-H activation/borylation methodology, in

Synthesis of Methyl Cyclopentanecarboxylate: A Laboratory Experience in Carbon Rearrangement

ERIC Educational Resources Information Center

Orchard, Alexandra; Maniquis, Roxanne V.; Salzameda, Nicholas T.

2016-01-01

We present a novel guided inquiry second semester organic chemistry laboratory rearrangement experiment. Students performed the Favorskii Rearrangement to obtain methyl cyclopentanecarboxylate in good yields. The students learned about the individual steps of the Favorskii mechanism and were required to propose a complete reaction mechanism and…

Advanced lung adenocarcinomas with ROS1-rearrangement frequently show hepatoid cell

PubMed Central

Kong, Mei; Zhou, Jianya; Ding, Wei; Zhou, Jianying

2016-01-01

Defining distinctive histologic characteristics of ROS1-rearranged non-small-cell lung carcinomas (NSCLCs) may help identify cases that merit molecular testing. However, the majority of previous reports have focused on surgical specimens but only limited studies assessed histomorphology of advanced NSCLCs. In order to identify the clinical and histological characteristics of ROS1-rearranged advanced NSCLCs, we examined five hundred sixteen Chinese patients with advanced NSCLCs using ROS1 fluorescence in situ hybridization and real-time polymerase chain reaction and then analyzed for clinical and pathological features. We performed univariate and multivariate analyses to identify predictive factors associated with ROS1 rearrangement. 19 tumors were identified with ROS1 rearrangement (3.7% of adenocarcinomas). 16 ROS1+ and 122 ROS1- samples with available medical records and enough tumor cells were included for histological analysis. Compared with ROS1-negative advanced NSCLCs, ROS1-rearranged advanced NSCLCs were associated with a younger age at presentation. ROS1 rearrangements were not significantly associated with sex, smoking history, drinking history and metastatic sites. The most common histological pattern was solid growth (12/16), followed by acinar (4/16) growth. 66.7% cases with solid growth pattern showed hepatoid cytology (8/12) and 75% cases with acinar growth pattern showed a cribriform structure (3/4). 18.8% cases were found to have abundant extracellular mucus or signet-ring cells (3/16). Only one case with solid growth pattern showed psammomatous calcifications. In conclusion, age, hepatoid cytology and cribriform structure are the independent predictors for ROS1-rearranged advanced NSCLCs, recognizing these may be helpful in finding candidates for genomic alterations, especially when available tissue samples are limited. PMID:27708233

Copper/amino acid catalyzed cross-couplings of aryl and vinyl halides with nucleophiles.

PubMed

Ma, Dawei; Cai, Qian

2008-11-18

Copper-assisted Ullmann-type coupling reactions are valuable transformations for organic synthesis. Researchers have extensively applied these reactions in both academic and industrial settings. However, two important issues, the high reaction temperatures (normally above 150 degrees C) and the stoichiometric amounts of copper necessary, have greatly limited the reaction scope. To solve these problems, we and other groups have recently explored the use of special ligands to promote these coupling reactions. We first showed that the structure of alpha-amino acids can accelerate Cu-assisted Ullmann reactions, leading to the coupling reactions of aryl halides and alpha-amino acids at 80-90 degrees C. In response to these encouraging results, we also discovered that an l-proline ligand facilitated the following transformations: (1) coupling of aryl halides with primary amines, cyclic secondary amines, and N-containing heterocycles at 40-90 degrees C; (2) coupling of aryl halides with sulfinic acid salts at 80-95 degrees C; (3) azidation of aryl halides and vinyl halides with sodium azide at 40-95 degrees C; (4) coupling of aryl halides with activated methylene compounds at 25-50 degrees C. In addition, we found that N,N-dimethylglycine as a ligand facilitated Cu-catalyzed biaryl ether formation at 90 degrees C. Moreover, Sonogashira reactions worked in the absence of palladium and phosphine ligands, forming enamides from vinyl halides and amides at temperatures ranging from ambient temperature up to 80 degrees C. Furthermore, we discovered that an ortho-amide group can accelerate some Ullmann-type reactions. This functional group in combination with other ligand effects allowed for aryl amination or biaryl ether formation at ambient temperature. The coupling between aryl halides and activated methylene compounds even proceeded at -45 degrees C to enantioselectively form a quaternary carbon center. Taking advantage of these results, we developed several novel approaches

Constitutional chromothripsis rearrangements involve clustered double-stranded DNA breaks and nonhomologous repair mechanisms.

PubMed

Kloosterman, Wigard P; Tavakoli-Yaraki, Masoumeh; van Roosmalen, Markus J; van Binsbergen, Ellen; Renkens, Ivo; Duran, Karen; Ballarati, Lucia; Vergult, Sarah; Giardino, Daniela; Hansson, Kerstin; Ruivenkamp, Claudia A L; Jager, Myrthe; van Haeringen, Arie; Ippel, Elly F; Haaf, Thomas; Passarge, Eberhard; Hochstenbach, Ron; Menten, Björn; Larizza, Lidia; Guryev, Victor; Poot, Martin; Cuppen, Edwin

2012-06-28

Chromothripsis represents a novel phenomenon in the structural variation landscape of cancer genomes. Here, we analyze the genomes of ten patients with congenital disease who were preselected to carry complex chromosomal rearrangements with more than two breakpoints. The rearrangements displayed unanticipated complexity resembling chromothripsis. We find that eight of them contain hallmarks of multiple clustered double-stranded DNA breaks (DSBs) on one or more chromosomes. In addition, nucleotide resolution analysis of 98 breakpoint junctions indicates that break repair involves nonhomologous or microhomology-mediated end joining. We observed that these eight rearrangements are balanced or contain sporadic deletions ranging in size between a few hundred base pairs and several megabases. The two remaining complex rearrangements did not display signs of DSBs and contain duplications, indicative of rearrangement processes involving template switching. Our work provides detailed insight into the characteristics of chromothripsis and supports a role for clustered DSBs driving some constitutional chromothripsis rearrangements. Copyright © 2012 The Authors. Published by Elsevier Inc. All rights reserved.

The ferroin-catalyzed Belousov-Zhabotinskii system with a "clock" behaviour

NASA Astrophysics Data System (ADS)

Melicherčík, Milan; Treindl, L̆udovít

1991-07-01

The ferroin-catalyzed Belousov-Zhabotinskii oscillatory system with methyl-, ethyl-, or isopropyl-ester of 3-oxobutanoic acid exhibits a "clock" behaviour and subsequent two-frequency oscillations. The influence of oxygen on the "clock" behaviour is assumed to be caused by an interaction of oxygen as a scavenger with intermediary radicals. A mechanism of the "clock" behaviour together with two-frequency oscillations of the Belousov-Zhabotinskii type will be developed later.

Carbanion-Accelerated Claisen Rearrangements Asymmetric Induction with Chiral Phosphorus-Stabilized Anions‡

PubMed Central

Denmark, Scott E.; Marlin, John E.; Rajendra, G.

2012-01-01

The carbanion-accelerated Claisen rearrangement has been extended to include phosphorus carbanion-stabilizing groups. The appropriately substituted allyl vinyl ethers are synthesized by the nucleophilic addition of allyloxides to phosphorus-substituted allenes, which are obtained in one step from simple starting materials. The phosphorus-stabilized, carbanion-accelerated Claisen rearrangements proceed rapidly at room temperature in high yield, and the rearrangements are highly site and stereoselective. The first examples of asymmetric induction in the Claisen rearrangement with chiral, phosphorus, anion-stabilizing groups are described. The observed asymmetric induction is highly dependent on the structure of the auxiliary and the metal counterion involved. Both internal and relative diastereoselectivity are high. A model for the observed sense of internal diastereoselectivity is proposed that is founded in the current understanding of the structure of phosphorus-stabilized anions. PMID:23101563

10 CFR 110.124 - Rearrangement or suspension of a hearing.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 2 2011-01-01 2011-01-01 false Rearrangement or suspension of a hearing. 110.124 Section 110.124 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) EXPORT AND IMPORT OF NUCLEAR EQUIPMENT AND MATERIAL Special Procedures for Classified Information in Hearings § 110.124 Rearrangement or suspension of...

10 CFR 110.124 - Rearrangement or suspension of a hearing.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 2 2010-01-01 2010-01-01 false Rearrangement or suspension of a hearing. 110.124 Section 110.124 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) EXPORT AND IMPORT OF NUCLEAR EQUIPMENT AND MATERIAL Special Procedures for Classified Information in Hearings § 110.124 Rearrangement or suspension of...

ALK-rearranged pulmonary adenocarcinoma in Thai Patients: From diagnosis to treatment efficacy.

PubMed

Incharoen, Pimpin; Reungwetwattana, Thanyanan; Saowapa, Sakditad; Kamprerasart, Kaettipong; Pangpunyakulchai, Duangjai; Arsa, Lalida; Jinawath, Artit

2016-05-03

Anaplastic lymphoma kinase (ALK) gene rearrangement is detected in 3% to 13% of non-small cell lung carcinoma patients, and these patients benefit from ALK inhibitors. The aim of this study was to determine the prevalence, the clinical and histological characteristics and the treatment outcomes of ALK-rearranged lung adenocarcinoma using immunohistochemistry (IHC) IHC, reverse transcription polymerase chain reaction (RT-PCR) and fluorescence in situ hybridization (FISH) methodologies. A total of 268 pulmonary adenocarcinoma patients were screened for ALK expression by ALK IHC, which was confirmed by FISH and/or RT-PCR for ALK gene rearrangement. The treatment outcomes of ALK-rearranged patients were retrospectively reviewed. ALK gene rearrangement was identified in 26 cases (9.7%) with no EGFR co-mutation, and it showed significant associations with younger age, female sex and non-smoker status (p < 0.05). A cribriform growth pattern was identified as the dominant histologic feature, and a solid signet ring cell component was focally present in a minority of the cases. Among 12 ALK-rearranged patients with conventional treatment, seven cases in the early stage of disease were cured and alive, and five patients in the late stage of the disease progressed and died, with a median overall survival (OS) at 14 months. Of the 14 patients receiving crizotinib, all of them had clinical benefit from crizotinib treatment, with one patient having a complete response (CR), 12 patients having a partial response (PR) and one patient having stable disease (SD). On the cutoff date, six of 14 patients were continuing crizotinib treatment with a median time of response of 7.5 (3-13) months, while eight patients had disease progression, and five of them died with a median OS at 8 months. ALK gene rearrangement tended to occur in younger, non-smoking, female patients. ALK IHC is a reliable screening method to detect ALK gene rearrangement. Crizotinib therapy provided treatment benefit

Iron-catalyzed olefin epoxidation in the presence of acetic acid: insights into the nature of the metal-based oxidant.

PubMed

Mas-Ballesté, Rubén; Que, Lawrence

2007-12-26

The iron complexes [(BPMEN)Fe(OTf)2] (1) and [(TPA)Fe(OTf)2] (2) [BPMEN = N,N'-bis-(2-pyridylmethyl)-N,N'-dimethyl-1,2-ethylenediamine; TPA = tris-(2-pyridylmethyl)amine] catalyze the oxidation of olefins by H2O2 to yield epoxides and cis-diols. The addition of acetic acid inhibits olefin cis-dihydroxylation and enhances epoxidation for both 1 and 2. Reactions carried out at 0 degrees C with 0.5 mol % catalyst and a 1:1.5 olefin/H2O2 ratio in a 1:2 CH3CN/CH3COOH solvent mixture result in nearly quantitative conversions of cyclooctene to epoxide within 1 min. The nature of the active species formed in the presence of acetic acid has been probed at low temperature. For 2, in the absence of substrate, [(TPA)FeIII(OOH)(CH3COOH)]2+ and [(TPA)FeIVO(NCCH3)]2+ intermediates can be observed. However, neither is the active epoxidizing species. In fact, [(TPA)FeIVO(NCCH3)]2+ is shown to form in competition with substrate oxidation. Consequently, it is proposed that epoxidation is mediated by [(TPA)FeV(O)(OOCCH3)]2+, generated from O-O bond heterolysis of the [(TPA)FeIII(OOH)(CH3COOH)]2+ intermediate, which is promoted by the protonation of the terminal oxygen atom of the hydroperoxide by the coordinated carboxylic acid.

Mg2+-dependent conformational changes and product release during DNA-catalyzed RNA ligation monitored by Bimane fluorescence

PubMed Central

Turriani, Elisa; Höbartner, Claudia; Jovin, Thomas M.

2015-01-01

Among the deoxyribozymes catalyzing the ligation of two RNA substrates, 7S11 generates a branched RNA containing a 2′,5′-linkage. We have attached the small fluorogenic probe Bimane to the triphosphate terminated RNA substrate and utilized emission intensity and anisotropy to follow structural rearrangements leading to a catalytically active complex upon addition of Mg2+. Bimane coupled to synthetic oligonucleotides is quenched by nearby guanines via photoinduced electron transfer. The degree of quenching is sensitive to changes in the base pairing of the residues involved and in their distances to the probe. These phenomena permit the characterization of various sequential processes in the assembly and function of 7S11: binding of Mg2+ to the triphosphate moiety, release of quenching of the probe by the 5′-terminal G residues of R-RNA as they engage in secondary base-pair interactions, local rearrangement into a distinct active conformation, and continuous release of the Bimane-labeled pyrophosphate during the course of reaction at 37°C. It was possible to assign equilibrium and rate constants and structural interpretations to the sequence of conformational transitions and catalysis, information useful for optimizing the design of next generation deoxyribozymes. The fluorescent signatures, thermodynamic equilibria and catalytic function of numerous mutated (base/substituted) molecules were examined. PMID:25505142

The rhodium catalyzed three-component reaction of diazoacetates, titanium(IV) alkoxides and aldehydes.

PubMed

Lu, Chong-Dao; Liu, Hui; Chen, Zhi-Yong; Hu, Wen-Hao; Mi, Ai-Qiao

2005-05-28

The rhodium(II)-catalyzed three-component reaction of diazoacetates, titanium alkoxides and aldehydes is shown to give alpha-alkoxyl-beta-hydroxyl acid derivatives; the novel C-C bond formation reaction is proposed to occur through oxonium ylides derived from diazo compounds and titanium alkoxides, and followed by intermolecular trapping by aldehydes.

A Prediction Model for ROS1-Rearranged Lung Adenocarcinomas based on Histologic Features

PubMed Central

Zheng, Jing; Kong, Mei; Sun, Ke; Wang, Bo; Chen, Xi; Ding, Wei; Zhou, Jianying

2016-01-01

Aims To identify the clinical and histological characteristics of ROS1-rearranged non-small-cell lung carcinomas (NSCLCs) and build a prediction model to prescreen suitable patients for molecular testing. Methods and Results We identified 27 cases of ROS1-rearranged lung adenocarcinomas in 1165 patients with NSCLCs confirmed by real-time PCR and FISH and performed univariate and multivariate analyses to identify predictive factors associated with ROS1 rearrangement and finally developed prediction model. Detected with ROS1 immunochemistry, 59 cases of 1165 patients had a certain degree of ROS1 expression. Among these cases, 19 cases (68%, 19/28) with 3+ and 8 cases (47%, 8/17) with 2+ staining were ROS1 rearrangement verified by real-time PCR and FISH. In the resected group, the acinar-predominant growth pattern was the most commonly observed (57%, 8/14), while in the biopsy group, solid patterns were the most frequently observed (78%, 7/13). Based on multiple logistic regression analysis, we determined that female sex, cribriform structure and the presence of psammoma body were the three most powerful indicators of ROS1 rearrangement, and we have developed a predictive model for the presence of ROS1 rearrangements in lung adenocarcinomas. Conclusions Female, cribriform structure and presence of psammoma body were the three most powerful indicator of ROS1 rearrangement status, and predictive formula was helpful in screening ROS1-rearranged NSCLC, especially for ROS1 immunochemistry equivocal cases. PMID:27648828

A Prediction Model for ROS1-Rearranged Lung Adenocarcinomas based on Histologic Features.

PubMed

Zhou, Jianya; Zhao, Jing; Zheng, Jing; Kong, Mei; Sun, Ke; Wang, Bo; Chen, Xi; Ding, Wei; Zhou, Jianying

2016-01-01

To identify the clinical and histological characteristics of ROS1-rearranged non-small-cell lung carcinomas (NSCLCs) and build a prediction model to prescreen suitable patients for molecular testing. We identified 27 cases of ROS1-rearranged lung adenocarcinomas in 1165 patients with NSCLCs confirmed by real-time PCR and FISH and performed univariate and multivariate analyses to identify predictive factors associated with ROS1 rearrangement and finally developed prediction model. Detected with ROS1 immunochemistry, 59 cases of 1165 patients had a certain degree of ROS1 expression. Among these cases, 19 cases (68%, 19/28) with 3+ and 8 cases (47%, 8/17) with 2+ staining were ROS1 rearrangement verified by real-time PCR and FISH. In the resected group, the acinar-predominant growth pattern was the most commonly observed (57%, 8/14), while in the biopsy group, solid patterns were the most frequently observed (78%, 7/13). Based on multiple logistic regression analysis, we determined that female sex, cribriform structure and the presence of psammoma body were the three most powerful indicators of ROS1 rearrangement, and we have developed a predictive model for the presence of ROS1 rearrangements in lung adenocarcinomas. Female, cribriform structure and presence of psammoma body were the three most powerful indicator of ROS1 rearrangement status, and predictive formula was helpful in screening ROS1-rearranged NSCLC, especially for ROS1 immunochemistry equivocal cases.

Silica metal-oxide vesicles catalyze comprehensive prebiotic chemistry.

PubMed

Bizzarri, Bruno Mattia; Botta, Lorenzo; Pérez-Valverde, Maritza Iveth; Saladino, Raffaele; Di Mauro, Ernesto; Garcia Ruiz, Juan Manuel

2018-03-30

It has recently been demonstrated that mineral self-assembled structures catalyzing prebiotic chemical reactions may form in natural waters derived from serpentinization, a geological process widespread in the early stages of Earth-like planets. We have synthesized self-assembled membranes by mixing microdrops of metal solutions with alkaline silicate solutions in the presence of formamide (NH2CHO), a single carbon molecule, at 80ºC. We found that these bilayer membranes, made of amorphous silica and metal oxide-hydroxide nanocrystals, catalyze the condensation of formamide, yielding the four nucleobases of RNA, three aminoacids and several carboxylic acids in a single pot experiment. Besides manganese, iron and magnesium, two abundant elements in the earliest Earth crust that are key in serpentinization reactions, are enough to produce all these biochemical compounds. These results suggest that the transition from inorganic geochemistry to prebiotic organic chemistry is common on a universal scale and, most probably, earlier than ever thought for our planet. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Contribution of canonical nonhomologous end joining to chromosomal rearrangements is enhanced by ATM kinase deficiency.

PubMed

Bhargava, Ragini; Carson, Caree R; Lee, Gabriella; Stark, Jeremy M

2017-01-24

A likely mechanism of chromosomal rearrangement formation involves joining the ends from two different chromosomal double-strand breaks (DSBs). These events could potentially be mediated by either of two end-joining (EJ) repair pathways [canonical nonhomologous end joining (C-NHEJ) or alternative end joining (ALT-EJ)], which cause distinct rearrangement junction patterns. The relative role of these EJ pathways during rearrangement formation has remained controversial. Along these lines, we have tested whether the DNA damage response mediated by the Ataxia Telangiectasia Mutated (ATM) kinase may affect the relative influence of C-NHEJ vs. ALT-EJ on rearrangement formation. We developed a reporter in mouse cells for a 0.4-Mbp deletion rearrangement that is formed by EJ between two DSBs induced by the Cas9 endonuclease. We found that disruption of the ATM kinase causes an increase in the frequency of the rearrangement as well as a shift toward rearrangement junctions that show hallmarks of C-NHEJ. Furthermore, ATM suppresses rearrangement formation in an experimental condition, in which C-NHEJ is the predominant EJ repair event (i.e., expression of the 3' exonuclease Trex2). Finally, several C-NHEJ factors are required for the increase in rearrangement frequency caused by inhibition of the ATM kinase. We also examined ATM effectors and found that H2AX shows a similar influence as ATM, whereas the influence of ATM on this rearrangement seems independent of 53BP1. We suggest that the contribution of the C-NHEJ pathway to the formation of a 0.4-Mbp deletion rearrangement is enhanced in ATM-deficient cells.

EFFECTIVE ACIDITY CONSTANT BEHAVIOR NEAR ZERO CHARGE CONDITIONS

EPA Science Inventory

Surface site (>SOH group) acidity reactions require expressions of the form: Ka = [>SOHn-1(z-1)]aH+EXP(-DG/RT)/[>SOHnz] (where all variables have their usual meaning). One can rearrange this expression to generate an effective acidity constant historically defined as: Qa = Ka...

Marsupials as models for understanding the role of chromosome rearrangements in evolution and disease.

PubMed

Deakin, Janine E; Kruger-Andrzejewska, Maya

2016-09-01

Chromosome rearrangements have been implicated in diseases, such as cancer, and speciation, but it remains unclear whether rearrangements are causal or merely a consequence of these processes. Two marsupial families with very different rates of karyotype evolution provide excellent models in which to study the role of chromosome rearrangements in a disease and evolutionary context. The speciose family Dasyuridae displays remarkable karyotypic conservation, with all species examined to date possessing nearly identical karyotypes. Despite the seemingly high degree of chromosome stability within this family, they appear prone to developing tumours, including transmissible devil facial tumours. In contrast, chromosome rearrangements have been frequent in the evolution of the species-rich family Macropodidae, which displays a high level of karyotypic diversity. In particular, the genus Petrogale (rock-wallabies) displays an extraordinary level of chromosome rearrangement among species. For six parapatric Petrogale species, it appears that speciation has essentially been caught in the act, providing an opportunity to determine whether chromosomal rearrangements are a cause or consequence of speciation in this system. This review highlights the reasons that these two marsupial families are excellent models for testing hypotheses for hotspots of chromosome rearrangement and deciphering the role of chromosome rearrangements in disease and speciation.

Mechanistic studies of ribonucleoside triphosphate reductase from Lactobacillus leichmannii

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harris, G.M.

1984-01-01

The mechanism of action of the adenosylcobalamin (AdoCbl)-dependent ribonucleoside triphosphate reductase (RTPR) was investigated using isotope effect and substrate specificity studies. These experiments were conducted on RTPR purified by a new method from Lactobacillus leichmannii. Isotope effect studies using (3{prime}-{sup 3}H)UTP and (3{prime}-{sup 3}H)ATP demonstrated that the 3{prime} C-H bond of the nucleotide is cleaved in order to cleave the 2{prime} C-OH bond. AdoCbl does not act as a direct H abstractor from the 3{prime} position of the substrate, but instead is thought to act as a radical chain initiator to generate an amino acid radical on the enzyme. Furthermore » support for this enzyme mediated cleavage of the 3{prime} C-H bond of the nucleotide and the novel role of AdoCbl came from studies using (3{prime}{sup 3}H)2{prime}-chloro-2{prime}-deoxyuridine 5{prime}-triphosphate ((3{prime}-{sup 3}H)CIUTP). Evidence is presented that during the course of this reaction, the {sup 3}H abstracted from the 3{prime} position of (3{prime}-{sup 3}H)CIUTP was either exchanged with the solvent or returned to the {beta} face of the 2{prime} position to produce (2{prime}{sup 3}H)-2{prime}-deoxy-3{prime}-ketoUTP. This result demonstrates that RTPR is capable of catalyzing a rearrangement reaction. The significance of the RTPR-catalyzed rearrangement with respect to the AdoCbl-dependent enzymes which catalyze rearrangements is discussed.« less

Synthesis of new β-amidodehydroaminobutyric acid derivatives and of new tyrosine derivatives using copper catalyzed C-N and C-O coupling reactions.

PubMed

Pereira, G; Vilaça, H; Ferreira, P M T

2013-02-01

Several β-amidodehydroaminobutyric acid derivatives were prepared from N,C-diprotected β-bromodehydroaminobutyric acids and amides by a copper catalyzed C-N coupling reaction. The best reaction conditions include the use of a catalytic amount of CuI, N,N'-dimethylethylenediamine as ligand and K(2)CO(3) as base in toluene at 110 °C. The stereochemistry of the products was determined using NOE difference experiments and the results obtained are in agreement with an E-stereochemistry. Thus, the stereochemistry is maintained in the case of the E-isomers of β-bromodehydroaminobutyric acid derivatives, but when the Z-isomers were used as substrates the reaction proceeds with inversion of configuration. The use of β-bromodehydrodipeptides as substrates was also tested. It was found that the reaction outcome depend on the stereochemistry of the β-bromodehydrodipeptide and on the nature of the first amino acid residue. The products isolated were the β-amidodehydrodipeptide derivatives and/or the corresponding dihydropyrazines. The same catalytic system (CuI/N,N'-dimethylethylene diamine) was used in the C-O coupling reactions between a tyrosine derivative and aryl bromides. The new O-aryltyrosine derivatives were isolated in moderate to good yields. The photophysical properties of two of these compounds were studied in four solvents of different polarity. The results show that these compounds after deprotection can be used as fluorescence markers.

Structure-reactivity relationship of Amadori rearrangement products compared to related ketoses.

PubMed

Kaufmann, Martin; Meissner, Philipp M; Pelke, Daniel; Mügge, Clemens; Kroh, Lothar W

2016-06-16

Structure-reactivity relationships of Amadori rearrangement products compared to their related ketoses were derived from multiple NMR spectroscopic techniques. Besides structure elucidation of six Amadori rearrangement products derived from d-glucose and d-galactose with l-alanine, l-phenylalanine and l-proline, especially quantitative (13)C selective saturation transfer NMR spectroscopy was applied to deduce information on isomeric systems. It could be shown exemplarily that the Amadori compound N-(1-deoxy-d-fructos-1-yl)-l-proline exhibits much higher isomerisation rates than d-fructose, which can be explained by C-1 substituent mediated intramolecular catalysis. In combination with a reduced carbonyl activity of Amadori compounds compared to their related ketoses which results in an increased acyclic keto isomer concentration, the results on isomerisation dynamics lead to a highly significant increased reactivity of Amadori compounds. This can be clearly seen, comparing approximated carbohydrate milieu stability time constants (ACuSTiC) which is 1 s for N-(1-deoxy-d-fructos-1-yl)-l-proline and 10 s for d-fructose at pD 4.20 ± 0.05 at 350 K. In addition, first NMR spectroscopic data are provided, which prove that α-pyranose of (amino acid substituted) d-fructose adopts both, (2)C5 and (5)C2 conformation. Copyright © 2016 Elsevier Ltd. All rights reserved.

Molybdenum Nitrogenase Catalyzes the Reduction and Coupling of CO to Form Hydrocarbons*♦

PubMed Central

Yang, Zhi-Yong; Dean, Dennis R.; Seefeldt, Lance C.

2011-01-01

The molybdenum-dependent nitrogenase catalyzes the multi-electron reduction of protons and N2 to yield H2 and 2NH3. It also catalyzes the reduction of a number of non-physiological doubly and triply bonded small molecules (e.g. C2H2, N2O). Carbon monoxide (CO) is not reduced by the wild-type molybdenum nitrogenase but instead inhibits the reduction of all substrates catalyzed by nitrogenase except protons. Here, we report that when the nitrogenase MoFe protein α-Val70 residue is substituted by alanine or glycine, the resulting variant proteins will catalyze the reduction and coupling of CO to form methane (CH4), ethane (C2H6), ethylene (C2H4), propene (C3H6), and propane (C3H8). The rates and ratios of hydrocarbon production from CO can be adjusted by changing the flux of electrons through nitrogenase, by substitution of other amino acids located near the FeMo-cofactor, or by changing the partial pressure of CO. Increasing the partial pressure of CO shifted the product ratio in favor of the longer chain alkanes and alkenes. The implications of these findings in understanding the nitrogenase mechanism and the relationship to Fischer-Tropsch production of hydrocarbons from CO are discussed. PMID:21454640

High Performance Solid Polymer Electrolytes for Rechargeable Batteries: A Self-Catalyzed Strategy toward Facile Synthesis.

PubMed

Cui, Yanyan; Liang, Xinmiao; Chai, Jingchao; Cui, Zili; Wang, Qinglei; He, Weisheng; Liu, Xiaochen; Liu, Zhihong; Cui, Guanglei; Feng, Jiwen

2017-11-01

It is urgent to seek high performance solid polymer electrolytes (SPEs) via a facile chemistry and simple process. The lithium salts are composed of complex anions that are stabilized by a Lewis acid agent. This Lewis acid can initiate the ring opening polymerization. Herein, a self-catalyzed strategy toward facile synthesis of crosslinked poly(ethylene glycol) diglycidyl ether-based solid polymer electrolyte (C-PEGDE) is presented. It is manifested that the poly(ethylene glycol) diglycidyl ether-based solid polymer electrolyte possesses a superior electrochemical stability window up to 4.5 V versus Li/Li + and considerable ionic conductivity of 8.9 × 10 -5 S cm -1 at ambient temperature. Moreover, the LiFePO 4 /C-PEGDE/Li batteries deliver stable charge/discharge profiles and considerable rate capability. It is demonstrated that this self-catalyzed strategy can be a very effective approach for high performance solid polymer electrolytes.

Behavior of S.A.P. in the Mercury Catalyzed Nitric Acid Dissolution; COMPORTAMENTO DEL S.A.P. ALL'ATTACCO DI SOLUZIONI DI ACIDO NITRICO E NITRATO MERCURICO

DOE Office of Scientific and Technical Information (OSTI.GOV)

Beone, G.

1963-10-01

Plates of S.A.P. (sintered Aluminum Powder) were dissolved under different conditions in a nitric acid solution containing mercuric nitrate as a catalyst. These experiments nim at establishing a head-end dissolution process for S.A.P. cladded uranium oxide fuels. The results of preliminary dissolution experiments on simulated fuel rods are also described. The behavior of S.A.P. in the mercury catalyzed nitric acid dissolutions differs strongly from the behavior of aluminum: reaction rates are very low for S.A.P. and the dissolution time borders on being unacceptable in an industrial process. Settling rates of suspended alumina are however favorable. A tentative head end flowsheetmore » lay out for PRO second core fuel elements is included. (auth)« less

[Lung adenocarcinoma with concomitant EGFR mutation and ALK rearrangement].

PubMed

Caliez, J; Monnet, I; Pujals, A; Rousseau-Bussac, G; Jabot, L; Boudjemaa, A; Leroy, K; Chouaid, C

2017-05-01

Among patients with non-small-cell lung cancer, coexistence of EGFR mutation and ALK rearrangement is rare. We describe the clinical features of two patients with this double anomaly. A 62-year-old Caucasian non-smoking woman was diagnosed with cT4N0M0 lung adenocarcinoma. Initial biopsy showed EGFR mutation and ALK rearrangement. She received cisplatin-gemcitabine, followed by 17 months of gemcitabine. Owing to progression, she received erlotinib for 14 months, then paclitaxel for 6 months and finally crizotinib. A partial response was achieved and maintained for 24 months. A 45-year-old Caucasian woman, light smoker, was diagnosed with cT2N3M0 lung adenocarcinoma. Only EGFR mutation was found on initial analysis. She underwent treatment with cisplatin-gemcitabine and thoracic radiotherapy. Progression occurred after 8 months and afatinbib was started. Eight months later, progression was observed with a neoplasic pleural effusion in which tumor cells expressing ALK rearrangement were found. A new FISH analysis was performed on the initial tumor but did not find this rearrangement. Despite a third line of crizotinib, the patient died one month later. The literature shows 45 other cases of these two abnormalities, observed either from the start or during follow-up. EGFR's TKI were almost always given before ALK's TKI. Therapeutic strategy needs to be clarified in cases of double alteration. With regard to the second patient, appearance of ALK rearrangement may constitute a resistance mechanism to EGFR's TKI. Copyright © 2016 SPLF. Published by Elsevier Masson SAS. All rights reserved.

Oncogenic rearrangements driving ionizing radiation–associated human cancer

PubMed Central

Santoro, Massimo; Carlomagno, Francesca

2013-01-01

The Chernobyl nuclear disaster has caused a remarkable increase in radiation-induced papillary thyroid carcinoma in children and young adults. In this issue of the JCI, Ricarte-Filho and colleagues demonstrate that chromosomal rearrangements are the oncogenic “drivers” in most post-Chernobyl carcinomas and that they often lead to unscheduled activation of the MAPK signaling pathway. These findings represent a major step forward in our understanding of radiation-induced carcinogenesis and suggest various hypotheses about the mechanisms underlying the formation and selection of gene rearrangements during cancer cell evolution. PMID:24162670

The He+H¯→He p¯+e+ rearrangement

NASA Astrophysics Data System (ADS)

Todd, Allan C.; Armour, Edward A. G.

2006-06-01

In this paper, we present a summary of our work in progress on calculating cross sections for the He+H¯→He p¯+e+ rearrangement process in He H¯ scattering. This has involved a study of the system He p¯ within the Born-Oppenheimer (BO) approximation using the Rayleigh-Ritz variational method. This work has been reported in [A.C. Todd, E.A.G. Armour, J. Phys. B 38 (2005) 3367] and is summarised here. Similar calculations are in progress for the He+H¯ entrance channel. We intend to use the entrance channel and rearrangement channel wave functions to obtain the cross sections for the rearrangement using the distorted wave Born approximation T-matrix method described elsewhere in these proceedings [E.A.G. Armour, S. Jonsell, Y. Liu, A.C. Todd, these Proceedings, doi:10.1016/j.nimb.2006.01.049].

Transglutaminase catalyzed cross-linking of sodium caseinate improves oxidative stability of flaxseed oil emulsion.

PubMed

Ma, Hairan; Forssell, Pirkko; Kylli, Petri; Lampi, Anna-Maija; Buchert, Johanna; Boer, Harry; Partanen, Riitta

2012-06-20

Sodium caseinate was modified by transglutaminase catalyzed cross-linking reaction prior to the emulsification process in order to study the effect of cross-linking on the oxidative stability of protein stabilized emulsions. The extent of the cross-linking catalyzed by different dosages of transglutaminase was investigated by following the ammonia production during the reaction and using SDS-PAGE gel. O/W emulsions prepared with the cross-linked and non-cross-linked sodium caseinates were stored for 30 days under the same conditions. Peroxide value measurement, oxygen consumption measurement, and headspace gas chromatography analysis were used to study the oxidative stability of the emulsions. The emulsion made of the cross-linked sodium caseinate showed an improved oxidative stability with reduced formation of fatty acid hydroperoxides and volatiles and a longer period of low rate oxygen consumption. The improving effect of transglutaminase catalyzed cross-linking could be most likely attributed to the enhanced physical stability of the interfacial protein layer against competitive adsorption by oil oxidation products.

A BAC clone fingerprinting approach to the detection of human genome rearrangements

PubMed Central

Krzywinski, Martin; Bosdet, Ian; Mathewson, Carrie; Wye, Natasja; Brebner, Jay; Chiu, Readman; Corbett, Richard; Field, Matthew; Lee, Darlene; Pugh, Trevor; Volik, Stas; Siddiqui, Asim; Jones, Steven; Schein, Jacquie; Collins, Collin; Marra, Marco

2007-01-01

We present a method, called fingerprint profiling (FPP), that uses restriction digest fingerprints of bacterial artificial chromosome clones to detect and classify rearrangements in the human genome. The approach uses alignment of experimental fingerprint patterns to in silico digests of the sequence assembly and is capable of detecting micro-deletions (1-5 kb) and balanced rearrangements. Our method has compelling potential for use as a whole-genome method for the identification and characterization of human genome rearrangements. PMID:17953769

Carbon Isotope Measurements of Experimentally-Derived Hydrothermal Mineral-Catalyzed Organic Products by Pyrolysis-Isotope Ratio Mass Spectrometry

NASA Technical Reports Server (NTRS)

Socki, Richard A.; Fu, Qi; Niles, Paul B.

2011-01-01

We report results of experiments to measure the C isotope composition of mineral catalyzed organic compounds derived from high temperature and high pressure synthesis. These experiments make use of an innovative pyrolysis technique designed to extract and measure C isotopes. To date, our experiments have focused on the pyrolysis and C isotope ratio measurements of low-molecular weight intermediary hydrocarbons (organic acids and alcohols) and serve as a proof of concept for making C and H isotope measurements on more complicated mixtures of solid-phase hydrocarbons and intermediary products produced during high temperature and high pressure synthesis on mineral-catalyzed surfaces. The impetus for this work stems from recently reported observations of methane detected within the Martian atmosphere [1-4], coupled with evidence showing extensive water-rock interaction during Martian history [5-7]. Methane production on Mars could be the result of synthesis by mineral surface-catalyzed reduction of CO2 and/or CO by Fischer-Tropsch Type (FTT) reactions during serpentization reactions [8,9]. Others have conducted experimental studies to show that FTT reactions are plausible mechanisms for low-molecular weight hydrocarbon formation in hydrothermal systems at mid-ocean ridges [10-12]. Further, recent experiments by Fu et al. [13] focus on examining detailed C isotope measurements of hydrocarbons produced by surface-catalyzed mineral reactions. Work described in this paper details the experimental techniques used to measure intermediary organic reaction products (alcohols and organic acids).

Theoretical study on mechanisms of structural rearrangement and ionic dissociation in the HCl(H 2O) 4 cluster with path-integral molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Sugawara, Shuichi; Yoshikawa, Takehiro; Takayanagi, Toshiyuki; Tachikawa, Masanori

2011-01-01

The structural rearrangement process for the HCl(H2O)4 cluster has been studied by path-integral molecular dynamics simulations, where 'on-the-fly' calculation of the potential energy surface is done with the PM3-MAIS semiempirical level. The mechanisms of the rearrangement were analyzed using appropriate collective coordinates as well as detailed potential energy diagrams derived from low-lying stationary points. It was found that the vibrational entropy mainly determines the stability of the cluster structure especially at high temperatures. We have also found that the acidity of HCl in the cluster correlates with the coordination number of chlorine with respect water molecules.

Tryptophanase from Proteus vulgaris: the conformational rearrangement in the active site, induced by the mutation of Tyrosine 72 to phenylalanine, and its mechanistic consequences.

PubMed

Kulikova, Vitalia V; Zakomirdina, Ludmila N; Dementieva, Irene S; Phillips, Robert S; Gollnick, Paul D; Demidkina, Tatyana V; Faleev, Nicolai G

2006-04-01

Tyr72 is located at the active site of tryptophanase (Trpase) from Proteus vulgaris. For the wild-type Trpase Tyr72 might be considered as the general acid catalyst at the stage of elimination of the leaving groups. The replacement of Tyr72 by Phe leads to a decrease in activity for L-tryptophan by 50,000-fold and to a considerable rearrangement of the active site of Trpase. This rearrangement leads to an increase of room around the alpha-C atom of any bound amino acid, such that covalent binding of alpha-methyl-substituted amino acids becomes possible (which cannot be realized in wild-type Trpase). The changes in reactivities of S-alkyl-L-cysteines provide evidence for an increase of congestion in the proximity of their side groups in the mutant enzyme as compared to wild-type enzyme. The observed alteration of catalytic properties in a large degree originates from a conformational change in the active site. The Y72F Trpase retains significant activity for L-serine, which allowed us to conclude that in the mutant enzyme, some functional group is present which fulfills the role of the general acid catalyst in reactions associated with elimination of small leaving groups.

Ligand-Promoted Rh(III)-Catalyzed Coupling of Aryl C-H Bonds with Arylboron Reagents.

PubMed

Wang, Huai-Wei; Cui, Pei-Pei; Lu, Yi; Sun, Wei-Yin; Yu, Jin-Quan

2016-04-15

Rhodium(III)-catalyzed C-H arylation of arenes with phenylboronic acid pinacol esters has been achieved using a readily removable N-pentafluorophenylbenzamide directing group for the first time. The use of a bidentate phosphine ligand (Binap) significantly increased the yield of the cross-coupling of C-H bonds with organoboron reagents.

Characterization of thermal and mechanical properties of opligo(glycerol-glutaric acid)s

USDA-ARS?s Scientific Manuscript database

Dibutyltin oxide was used to catalyze the synthesis of oligo(glycerol-glutaric acid)s in the absence and presence of solvent. Reaction times were either 10h or 24h for reactions performed in DMF and 24h for the neat reaction. The oligomers were obtained on average in 84% yield and were characteriz...

The initial step in the archaeal aspartate biosynthetic pathway catalyzed by a monofunctional aspartokinase

PubMed Central

Faehnle, Christopher R.; Liu, Xuying; Pavlovsky, Alexander; Viola, Ronald E.

2006-01-01

The activation of the β-carboxyl group of aspartate catalyzed by aspartokinase is the commitment step to amino-acid biosynthesis in the aspartate pathway. The first structure of a microbial aspartokinase, that from Methanococcus jannaschii, has been determined in the presence of the amino-acid substrate l-­aspartic acid and the nucleotide product MgADP. The enzyme assembles into a dimer of dimers, with the interfaces mediated by both the N- and C-terminal domains. The active-site functional groups responsible for substrate binding and specificity have been identified and roles have been proposed for putative catalytic functional groups. PMID:17012784

Identification of non-heme diiron proteins that catalyze triple bond and epoxy group formation.

PubMed

Lee, M; Lenman, M; Banaś, A; Bafor, M; Singh, S; Schweizer, M; Nilsson, R; Liljenberg, C; Dahlqvist, A; Gummeson, P O; Sjödahl, S; Green, A; Stymne, S

1998-05-08

Acetylenic bonds are present in more than 600 naturally occurring compounds. Plant enzymes that catalyze the formation of the Delta12 acetylenic bond in 9-octadecen-12-ynoic acid and the Delta12 epoxy group in 12,13-epoxy-9-octadecenoic acid were characterized, and two genes, similar in sequence, were cloned. When these complementary DNAs were expressed in Arabidopsis thaliana, the content of acetylenic or epoxidated fatty acids in the seeds increased from 0 to 25 or 15 percent, respectively. Both enzymes have characteristics similar to the membrane proteins containing non-heme iron that have histidine-rich motifs.

Transition metal-catalyzed oxidation of sulfur(IV) oxides. Atmospheric-relevant processes and mechanisms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brandt, C.; Eldik, R. van

1995-01-01

The transition metal-catalyzed oxidation of sulfur(IV) oxides has been known for more than 100 years. There is a significant lack of information on the actual role of the transition metal-catalyzed reactions, and much of the earlier work was performed without a detailed knowledge of the chemical system. For this reason attention is focused on the role of transition metal ions in the oxidation of sulfur(IV) oxides in terms of the coordination chemistry involved, as well as the stability and chemical behavior of the various participating species. The oxidation process of sulfur(IV) oxides plays an important role in atmospheric chemistry (e.g.more » acid rain formation) as well as industrial processes (e.g. desulfurization of plume gases and ore). The present report deals with the mechanism of the transition metal-catalyzed oxidation of sulfur(IV) oxides with the aim to discuss this in terms of atmospheric and chemical processes. In addition, the authors would like to emphasize the key role of oxygen in these processes. 1,076 refs.« less

Iodine-Catalyzed Isomerization of Dimethyl Muconate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Settle, Amy E.; Berstis, Laura; Zhang, Shuting

cis,cis-Muconic acid is a platform biobased chemical that can be upgraded to drop-in commodity and novel monomers. Among the possible drop-in products, dimethyl terephthalate can be synthesized via esterification, isomerization, Diels-Alder cycloaddition, and dehydrogenation. The isomerization of cis,cis-dimethyl muconate ( ccDMM) to the trans,trans-form ( ttDMM) can be catalyzed by iodine; however, studies have yet to address (i) the mechanism and reaction barriers unique to DMM, and (ii) the influence of solvent, potential for catalyst recycle, and recovery of high-purity ttDMM. To address this gap, we apply a joint computational and experimental approach to investigate iodine-catalyzed isomerization of DMM. Densitymore » functional theory calculations identified unique regiochemical considerations due to the large number of halogen-diene coordination schemes. Both transition state theory and experiments estimate significant barrier reductions with photodissociated iodine. Solvent selection was critical for rapid kinetics, likely due to solvent complexation with iodine. Under select conditions, ttDMM yields of 95% were achieved in <1 h with methanol, followed by high purity recovery (>98%) with crystallization. Lastly, post-reaction iodine can be recovered and recycled with minimal loss of activity. Altogether, these findings provide new insight into the mechanism and conditions necessary for DMM isomerization with iodine to advance the state-of-the-art for biobased chemicals.« less

Iodine-Catalyzed Isomerization of Dimethyl Muconate

DOE PAGES

Settle, Amy E.; Berstis, Laura; Zhang, Shuting; ...

2018-04-16

cis,cis-Muconic acid is a platform biobased chemical that can be upgraded to drop-in commodity and novel monomers. Among the possible drop-in products, dimethyl terephthalate can be synthesized via esterification, isomerization, Diels-Alder cycloaddition, and dehydrogenation. The isomerization of cis,cis-dimethyl muconate ( ccDMM) to the trans,trans-form ( ttDMM) can be catalyzed by iodine; however, studies have yet to address (i) the mechanism and reaction barriers unique to DMM, and (ii) the influence of solvent, potential for catalyst recycle, and recovery of high-purity ttDMM. To address this gap, we apply a joint computational and experimental approach to investigate iodine-catalyzed isomerization of DMM. Densitymore » functional theory calculations identified unique regiochemical considerations due to the large number of halogen-diene coordination schemes. Both transition state theory and experiments estimate significant barrier reductions with photodissociated iodine. Solvent selection was critical for rapid kinetics, likely due to solvent complexation with iodine. Under select conditions, ttDMM yields of 95% were achieved in <1 h with methanol, followed by high purity recovery (>98%) with crystallization. Lastly, post-reaction iodine can be recovered and recycled with minimal loss of activity. Altogether, these findings provide new insight into the mechanism and conditions necessary for DMM isomerization with iodine to advance the state-of-the-art for biobased chemicals.« less

High Performance Solid Polymer Electrolytes for Rechargeable Batteries: A Self‐Catalyzed Strategy toward Facile Synthesis

PubMed Central

Cui, Yanyan; Liang, Xinmiao; Chai, Jingchao; Cui, Zili; Wang, Qinglei; He, Weisheng; Liu, Xiaochen; Feng, Jiwen

2017-01-01

Abstract It is urgent to seek high performance solid polymer electrolytes (SPEs) via a facile chemistry and simple process. The lithium salts are composed of complex anions that are stabilized by a Lewis acid agent. This Lewis acid can initiate the ring opening polymerization. Herein, a self‐catalyzed strategy toward facile synthesis of crosslinked poly(ethylene glycol) diglycidyl ether‐based solid polymer electrolyte (C‐PEGDE) is presented. It is manifested that the poly(ethylene glycol) diglycidyl ether‐based solid polymer electrolyte possesses a superior electrochemical stability window up to 4.5 V versus Li/Li+ and considerable ionic conductivity of 8.9 × 10−5 S cm−1 at ambient temperature. Moreover, the LiFePO4/C‐PEGDE/Li batteries deliver stable charge/discharge profiles and considerable rate capability. It is demonstrated that this self‐catalyzed strategy can be a very effective approach for high performance solid polymer electrolytes. PMID:29201612

Yield of 1,6-anhydro-3,4-dideoxy-β-D-glycero-hex-3-enopyranos-2-ulose (levoglucosenone) on the acid-catalyzed pyrolysis of cellulose and 1,6-anhydro-β-D-glucopyranose (levoglucosan)

Treesearch

Abraham Broido; Malcolm Evett; Craig C. Hodges

1975-01-01

Although 1,6-anhydro-3,4-dideoxy-β-D-glycero-hex-3-enopyranos-2-ulose (2) is produced by the acid-catalyzed pyrolysis of both cellulose and 1,6-anhydro-β-D-glucopyranose (1), data presented here show that the principal mechanism of its formation in the pyrolysis of cellulose is not via 1. Furthermore, the data provide evidence that 1 itself is not...

Rearranged hopanes in sediments and petroleum

NASA Astrophysics Data System (ADS)

Moldowan, J. Michael; Fago, Frederick J.; Carlson, Robert M. K.; Young, Donald C.; an Duvne, Greg; Clardy, Jon; Schoell, Martin; Pillinger, Colin T.; Watt, David S.

1991-11-01

Two new rearranged hopanoid hydrocarbons have been isolated from a Prudhoe Bay crude, Alaska. 17α(H)-15α-methyl-27-norhopane was determined by X-ray crystallography. It is the first identified member of a new series of rearranged hopanes we propose to call "17α(H)-diahopanes." Analysis by gas chromatography-mass spectrometry - mass spectrometry (GC-MS-MS) of the parents of m/z 191 in several crudes suggests that this compound is a member of a C 29-C 34 series of 17α(H)-diahopanes common to many crude oils and sediments. In addition, a new member of the 18α(H)-neohopane series has also been elucidated. Determination of 18α(H)-17α-methyl-28,30-dinorhopane [18α(H)-30-norneohopane ], which we propose to nickname "C 29Ts," hinged upon advanced nuclear magnetic resonance (NMR) techniques (at 500 and 600 MHz) such as proton-detected 1H- 13C correlated spectra for the C-skeleton and Rotating-frame Overhauser Enhancement Spectroscopy (ROESY) for stereochemistry, as well as several other two-dimensional (2D) NMR techniques. This compound is the second known pseudohomolog of the neohopane series (together with 18α(H),22,29,30-trisnorneohopane, Ts), but the existence of additional pseudohomologs is still not clear. The structures of these rearranged hopanes are consistent with an origin by catalytic rearrangement from hopenes during early diagenesis. Carbon isotopic data collected on Ts, 17α(H)-diahopane, C 29Ts, 17α(H)-22,29,30-trisnorhopane (Tm), 17α(H)-30-norhopane, and 17α(H)-hopane isolated from the Prudhoe Bay oil are in the -27 to -28%o δ 13C range supporting mechanistic arguments based on structures that all are derived from common precursors. These δ 13C values are slightly more positive than the whole Prudhoe Bay oil (-30.1%), suggesting that these hopanes may have been derived from heterotrophic or cyanobacteria in the paleoecosystem during deposition of its source rock. Molecular mechanics calculations predict relative thermal stabilities in the

Iodide-ion-induced oscillations of the ferroin-catalyzed Belousov—Zhabotinskii reaction

NASA Astrophysics Data System (ADS)

Melicherčík, Milan; Treindl, Ľudovít

1992-08-01

Contrary to "classical" Belousov—Zhabotinskii (BZ) oscillatory systems, consisting of malonic acid, Ce(IV)—Ce(III) or Mn(III)—Mn(II) redox catalyst and KBrO 3 in solutions of H 2SO 4, where in an interval of added iodide initial concentrations 10 -4 mol dm -3 < [I -] 0 < 10 -3 mol dm -3 the oscillations have the same frequency and amplitude as in the absence of iodide, the effect of added iodide on the ferroin-catalyzed BZ system with methyl ester of 3-oxobutanoic acid leads to an increase in the number of oscillations and in the time of their duration. The dependence of this effect on substrate, bromate, iodide, sulfuric acid and ferroin concentrations has been studied. The observations may be explained by a mechanism involving direct reduction of ferroin by iodide, oxidation of iodide to iodate by bromate with a bromide production and eventual faster bromination and iodination of methyl ester of 3-oxobutanoic acid in relation to malonic acid.

Gold(I)-assisted catalysis - a comprehensive view on the [3,3]-sigmatropic rearrangement of allyl acetate

NASA Astrophysics Data System (ADS)

Freindorf, Marek; Cremer, Dieter; Kraka, Elfi

2018-03-01

The unified reaction valley approach (URVA) combined with the local mode, ring puckering and electron density analysis is applied to elucidate the mechanistic differences of the non-catalysed and the Au[I]-N-heterocyclic carbene (NHC)-catalysed [3,3]-sigmatropic rearrangement of allyl acetate. Using a dual-level approach (DFT and DLPNO-CCSD(T)), the influence of solvation, counter-ions, bulky and electron withdrawing/donating substituents as well as the exchange of the Au[I]-NHC with a Au[I]-phosphine catalyst is investigated. The catalyst breaks up the rearrangement into two steps by switching between Au[I]-π and Au[I]-σ complexation, thus avoiding the energy-consuming CO cleavage in the first step. Based on local stretching force constants ka(C=C), we derive for the first time a quantitative measure of the π-acidity of the Au[I] catalyst; in all catalysed reactions, the bond order n(C=C) drops from 2 to 1.65. The ring puckering analysis clarifies that all reactions start and end via a six-membered ring with a boat form. All Au[I]-σ-complex intermediates show a considerable admixture of the chair form. The non-catalysed [3,3]-sigmatropic rearrangement goes through a maximum of charge separation between the allyl and acetate units at the transition state, while all catalysed reactions proceed via a minimum of charge separation reached in the region of the Au[I]-σ-complex.

Clinical Activity of Alectinib in Advanced RET-Rearranged Non-Small Cell Lung Cancer.

PubMed

Lin, Jessica J; Kennedy, Elizabeth; Sequist, Lecia V; Brastianos, Priscilla K; Goodwin, Kelly E; Stevens, Sara; Wanat, Alexandra C; Stober, Lisa L; Digumarthy, Subba R; Engelman, Jeffrey A; Shaw, Alice T; Gainor, Justin F

2016-11-01

Chromosomal rearrangements involving rearranged during transfection gene (RET) occur in 1% to 2% of NSCLCs and may confer sensitivity to rearranged during transfection (RET) inhibitors. Alectinib is an anaplastic lymphoma kinase tyrosine kinase inhibitor (TKI) that also has anti-RET activity in vitro. The clinical activity of alectinib in patients with RET-rearranged NSCLC has not yet been reported. We have described four patients with advanced RET-rearranged NSCLC who were treated with alectinib (600 mg twice daily [n = 3] or 900 mg twice daily [n = 1]) as part of single-patient compassionate use protocols or off-label use of the commercially available drug. Four patients with metastatic RET-rearranged NSCLC were identified. Three of the four had received prior RET TKIs, including cabozantinib and experimental RET inhibitors. In total, we observed two (50%) objective radiographic responses after treatment with alectinib (one confirmed and one unconfirmed), with durations of therapy of 6 months and more than 5 months (treatment ongoing), respectively. Notably, one of these two patients had his dose of alectinib escalated to 900 mg twice daily and had clinical improvement in central nervous system metastases. In addition, one patient (25%) experienced a best response of stable disease lasting approximately 6 weeks (the drug discontinued for toxicity). A fourth patient who was RET TKI-naive had primary progression while receiving alectinib. Alectinib demonstrated preliminary antitumor activity in patients with advanced RET-rearranged NSCLC, most of whom had received prior RET inhibitors. Larger prospective studies with longer follow-up are needed to assess the efficacy of alectinib in RET-rearranged NSCLC and other RET-driven malignancies. In parallel, development of more selective, potent RET TKIs is warranted. Copyright © 2016 International Association for the Study of Lung Cancer. Published by Elsevier Inc. All rights reserved.

Lipase-catalyzed synthesis of fatty acid amide (erucamide) using fatty acid and urea.

PubMed

Awasthi, Neeraj Praphulla; Singh, R P

2007-01-01

Ammonolysis of fatty acids to the corresponding fatty acid amides is efficiently catalysed by Candida antartica lipase (Novozym 435). In the present paper lipase-catalysed synthesis of erucamide by ammonolysis of erucic acid and urea in organic solvent medium was studied and optimal conditions for fatty amides synthesis were established. In this process erucic acid gave 88.74 % pure erucamide after 48 hour and 250 rpm at 60 degrees C with 1:4 molar ratio of erucic acid and urea, the organic solvent media is 50 ml tert-butyl alcohol (2-methyl-2-propanol). This process for synthesis is economical as we used urea in place of ammonia or other amidation reactant at atmospheric pressure. The amount of catalyst used is 3 %.

Ruthenium(III) catalyzed oxidation of sugar alcohols by dichloroisocyanuric acid—A kinetic study

NASA Astrophysics Data System (ADS)

Lakshman Kumar, Y.; Venkata Nadh, R.; Radhakrishnamurti, P. S.

2016-02-01

Kinetics of ruthenium(III) catalyzed oxidation of biologically important sugar alcohols (myo-inositol, D-sorbitol, and D-mannitol) by dichloroisocyanuric acid was carried out in aqueous acetic acid—perchloric medium. The reactions were found to be first order in case of oxidant and ruthenium(III). Zero order was observed with the concentrations of sorbitol and mannitol whereas, a positive fractional order was found in the case of inositol concentration. An inverse fractional order was observed with perchloric acid in oxidation of three substrates. Arrhenius parameters were calculated and a plausible mechanism was proposed.

Copper-Catalyzed, Directing Group-Assisted Fluorination of Arene and Heteroarene C-H Bonds

PubMed Central

Truong, Thanh; Klimovica, Kristine; Daugulis, Olafs

2013-01-01

We have developed a method for direct, copper-catalyzed, auxiliary-assisted fluorination of β-sp2 C-H bonds of benzoic acid derivatives and γ-sp2 C-H bonds of α,α-disubstituted benzylamine derivatives. The reaction employs CuI catalyst, AgF fluoride source, and DMF, pyridine, or DMPU solvent at moderately elevated temperatures. Selective mono- or difluorination can be achieved by simply changing reaction conditions. The method shows excellent functional group tolerance and provides a straightforward way for the preparation of ortho-fluorinated benzoic acids. PMID:23758609

Translocations, inversions and other chromosome rearrangements.

PubMed

Morin, Scott J; Eccles, Jennifer; Iturriaga, Amanda; Zimmerman, Rebekah S

2017-01-01

Chromosomal rearrangements have long been known to significantly impact fertility and miscarriage risk. Advancements in molecular diagnostics are challenging contemporary clinicians and patients in accurately characterizing the reproductive risk of a given abnormality. Initial attempts at preimplantation genetic diagnosis were limited by the inability to simultaneously evaluate aneuploidy and missed up to 70% of aneuploidy in chromosomes unrelated to the rearrangement. Contemporary platforms are more accurate and less susceptible to technical errors. These techniques also offer the ability to improve outcomes through diagnosis of uniparental disomy and may soon be able to consistently distinguish between normal and balanced translocation karyotypes. Although an accurate projection of the anticipated number of unbalanced embryos is not possible at present, confirmation of normal/balanced status results in high pregnancy rates (PRs) and diagnostic accuracy. Copyright © 2016 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

Sampling and counting genome rearrangement scenarios

PubMed Central

2015-01-01

Background Even for moderate size inputs, there are a tremendous number of optimal rearrangement scenarios, regardless what the model is and which specific question is to be answered. Therefore giving one optimal solution might be misleading and cannot be used for statistical inferring. Statistically well funded methods are necessary to sample uniformly from the solution space and then a small number of samples are sufficient for statistical inferring. Contribution In this paper, we give a mini-review about the state-of-the-art of sampling and counting rearrangement scenarios, focusing on the reversal, DCJ and SCJ models. Above that, we also give a Gibbs sampler for sampling most parsimonious labeling of evolutionary trees under the SCJ model. The method has been implemented and tested on real life data. The software package together with example data can be downloaded from http://www.renyi.hu/~miklosi/SCJ-Gibbs/ PMID:26452124

Response to ERBB3-Directed Targeted Therapy in NRG1-Rearranged Cancers.

PubMed

Drilon, Alexander; Somwar, Romel; Mangatt, Biju P; Edgren, Henrik; Desmeules, Patrice; Ruusulehto, Anja; Smith, Roger S; Delasos, Lukas; Vojnic, Morana; Plodkowski, Andrew J; Sabari, Joshua; Ng, Kenneth; Montecalvo, Joseph; Chang, Jason; Tai, Huichun; Lockwood, William W; Martinez, Victor; Riely, Gregory J; Rudin, Charles M; Kris, Mark G; Arcila, Maria E; Matheny, Christopher; Benayed, Ryma; Rekhtman, Natasha; Ladanyi, Marc; Ganji, Gopinath

2018-06-01

NRG1 rearrangements are oncogenic drivers that are enriched in invasive mucinous adenocarcinomas (IMA) of the lung. The oncoprotein binds ERBB3-ERBB2 heterodimers and activates downstream signaling, supporting a therapeutic paradigm of ERBB3/ERBB2 inhibition. As proof of concept, a durable response was achieved with anti-ERBB3 mAb therapy (GSK2849330) in an exceptional responder with an NRG1 -rearranged IMA on a phase I trial (NCT01966445). In contrast, response was not achieved with anti-ERBB2 therapy (afatinib) in four patients with NRG1 -rearranged IMA (including the index patient post-GSK2849330). Although in vitro data supported the use of either ERBB3 or ERBB2 inhibition, these clinical results were consistent with more profound antitumor activity and downstream signaling inhibition with anti-ERBB3 versus anti-ERBB2 therapy in an NRG1 -rearranged patient-derived xenograft model. Analysis of 8,984 and 17,485 tumors in The Cancer Genome Atlas and MSK-IMPACT datasets, respectively, identified NRG1 rearrangements with novel fusion partners in multiple histologies, including breast, head and neck, renal, lung, ovarian, pancreatic, prostate, and uterine cancers. Significance: This series highlights the utility of ERBB3 inhibition as a novel treatment paradigm for NRG1 -rearranged cancers. In addition, it provides preliminary evidence that ERBB3 inhibition may be more optimal than ERBB2 inhibition. The identification of NRG1 rearrangements across various solid tumors supports a basket trial approach to drug development. Cancer Discov; 8(6); 686-95. ©2018 AACR. See related commentary by Wilson and Politi, p. 676 This article is highlighted in the In This Issue feature, p. 663 . ©2018 American Association for Cancer Research.

The History of Bordetella pertussis Genome Evolution Includes Structural Rearrangement

PubMed Central

Peng, Yanhui; Loparev, Vladimir; Batra, Dhwani; Bowden, Katherine E.; Burroughs, Mark; Cassiday, Pamela K.; Davis, Jamie K.; Johnson, Taccara; Juieng, Phalasy; Knipe, Kristen; Mathis, Marsenia H.; Pruitt, Andrea M.; Rowe, Lori; Sheth, Mili; Tondella, M. Lucia; Williams, Margaret M.

2017-01-01

ABSTRACT Despite high pertussis vaccine coverage, reported cases of whooping cough (pertussis) have increased over the last decade in the United States and other developed countries. Although Bordetella pertussis is well known for its limited gene sequence variation, recent advances in long-read sequencing technology have begun to reveal genomic structural heterogeneity among otherwise indistinguishable isolates, even within geographically or temporally defined epidemics. We have compared rearrangements among complete genome assemblies from 257 B. pertussis isolates to examine the potential evolution of the chromosomal structure in a pathogen with minimal gene nucleotide sequence diversity. Discrete changes in gene order were identified that differentiated genomes from vaccine reference strains and clinical isolates of various genotypes, frequently along phylogenetic boundaries defined by single nucleotide polymorphisms. The observed rearrangements were primarily large inversions centered on the replication origin or terminus and flanked by IS481, a mobile genetic element with >240 copies per genome and previously suspected to mediate rearrangements and deletions by homologous recombination. These data illustrate that structural genome evolution in B. pertussis is not limited to reduction but also includes rearrangement. Therefore, although genomes of clinical isolates are structurally diverse, specific changes in gene order are conserved, perhaps due to positive selection, providing novel information for investigating disease resurgence and molecular epidemiology. IMPORTANCE Whooping cough, primarily caused by Bordetella pertussis, has resurged in the United States even though the coverage with pertussis-containing vaccines remains high. The rise in reported cases has included increased disease rates among all vaccinated age groups, provoking questions about the pathogen's evolution. The chromosome of B. pertussis includes a large number of repetitive mobile

Breakpoint Features of Genomic Rearrangements in Neuroblastoma with Unbalanced Translocations and Chromothripsis

PubMed Central

Daveau, Romain; Combaret, Valérie; Pierre-Eugène, Cécile; Cazes, Alex; Louis-Brennetot, Caroline; Schleiermacher, Gudrun; Ferrand, Sandrine; Pierron, Gaëlle; Lermine, Alban; Frio, Thomas Rio; Raynal, Virginie; Vassal, Gilles; Barillot, Emmanuel; Delattre, Olivier; Janoueix-Lerosey, Isabelle

2013-01-01

Neuroblastoma is a pediatric cancer of the peripheral nervous system in which structural chromosome aberrations are emblematic of aggressive tumors. In this study, we performed an in-depth analysis of somatic rearrangements in two neuroblastoma cell lines and two primary tumors using paired-end sequencing of mate-pair libraries and RNA-seq. The cell lines presented with typical genetic alterations of neuroblastoma and the two tumors belong to the group of neuroblastoma exhibiting a profile of chromothripsis. Inter and intra-chromosomal rearrangements were identified in the four samples, allowing in particular characterization of unbalanced translocations at high resolution. Using complementary experiments, we further characterized 51 rearrangements at the base pair resolution that revealed 59 DNA junctions. In a subset of cases, complex rearrangements were observed with templated insertion of fragments of nearby sequences. Although we did not identify known particular motifs in the local environment of the breakpoints, we documented frequent microhomologies at the junctions in both chromothripsis and non-chromothripsis associated breakpoints. RNA-seq experiments confirmed expression of several predicted chimeric genes and genes with disrupted exon structure including ALK, NBAS, FHIT, PTPRD and ODZ4. Our study therefore indicates that both non-homologous end joining-mediated repair and replicative processes may account for genomic rearrangements in neuroblastoma. RNA-seq analysis allows the identification of the subset of abnormal transcripts expressed from genomic rearrangements that may be involved in neuroblastoma oncogenesis. PMID:23991058

Thermodynamics of Enzyme-Catalyzed Reactions Database

National Institute of Standards and Technology Data Gateway

SRD 74 Thermodynamics of Enzyme-Catalyzed Reactions Database (Web, free access)   The Thermodynamics of Enzyme-Catalyzed Reactions Database contains thermodynamic data on enzyme-catalyzed reactions that have been recently published in the Journal of Physical and Chemical Reference Data (JPCRD). For each reaction the following information is provided: the reference for the data, the reaction studied, the name of the enzyme used and its Enzyme Commission number, the method of measurement, the data and an evaluation thereof.

Rearrangement of mitochondrial tRNA genes in flat bugs (Hemiptera: Aradidae).

PubMed

Song, Fan; Li, Hu; Shao, Renfu; Shi, Aimin; Bai, Xiaoshuan; Zheng, Xiaorong; Heiss, Ernst; Cai, Wanzhi

2016-05-16

The typical insect mitochondrial (mt) genome organization, which contains a single chromosome with 37 genes, was found in the infraorder Pentatomomorpha (suborder Heteroptera). The arrangement of mt genes in these true bugs is usually the same as the ancestral mt gene arrangement of insects. Rearrangement of transfer RNA (tRNA) genes, however, has been found in two subfamilies of flat bugs (Mezirinae and Calisiinae, family Aradidae). In this study, we sequenced the complete mt genomes of four species from three other subfamilies (Aradinae, Carventinae and Aneurinae). We found tRNA gene rearrangement in all of these four species. All of the rearranged tRNA genes are located between the mitochondrial control region and cox1, indicating this region as a hotspot for gene rearrangement in flat bugs; the rearrangement is likely caused by events of tandem duplication and random deletion of genes. Furthermore, our phylogenetic and dating analyses indicated that the swap of positions between trnQ and trnI occurred ~162 million years ago (MYA) in the most recent common ancestor of the five subfamilies of flat bugs investigated to date, whereas the swap of positions between trnC and trnW occurred later in the lineage leading to Calisiinae, and the translocation of trnC and trnY occurred later than 134 MYA in the lineage leading to Aradinae.

Rearrangement of mitochondrial tRNA genes in flat bugs (Hemiptera: Aradidae)

PubMed Central

Song, Fan; Li, Hu; Shao, Renfu; Shi, Aimin; Bai, Xiaoshuan; Zheng, Xiaorong; Heiss, Ernst; Cai, Wanzhi

2016-01-01

The typical insect mitochondrial (mt) genome organization, which contains a single chromosome with 37 genes, was found in the infraorder Pentatomomorpha (suborder Heteroptera). The arrangement of mt genes in these true bugs is usually the same as the ancestral mt gene arrangement of insects. Rearrangement of transfer RNA (tRNA) genes, however, has been found in two subfamilies of flat bugs (Mezirinae and Calisiinae, family Aradidae). In this study, we sequenced the complete mt genomes of four species from three other subfamilies (Aradinae, Carventinae and Aneurinae). We found tRNA gene rearrangement in all of these four species. All of the rearranged tRNA genes are located between the mitochondrial control region and cox1, indicating this region as a hotspot for gene rearrangement in flat bugs; the rearrangement is likely caused by events of tandem duplication and random deletion of genes. Furthermore, our phylogenetic and dating analyses indicated that the swap of positions between trnQ and trnI occurred ~162 million years ago (MYA) in the most recent common ancestor of the five subfamilies of flat bugs investigated to date, whereas the swap of positions between trnC and trnW occurred later in the lineage leading to Calisiinae, and the translocation of trnC and trnY occurred later than 134 MYA in the lineage leading to Aradinae. PMID:27180804

Oligomerization of L-gamma-carboxyglutamic acid

NASA Technical Reports Server (NTRS)

Hill, A. R. Jr; Orgel, L. E.; Bada, J. L. (Principal Investigator)

1999-01-01

Unlike glutamic acid, L-gamma-carboxyglutamic acid does not oligomerize efficiently when treated with carbonyldiimidazole in aqueous solution. However, divalent ions such as Mg2+ catalyze the reaction, and lead to the formation of oligomers in good yield. In the presence of hydroxylapatite, L-gamma-carboxyglutamic acid oligomerizes efficiently in a reaction that proceeds in the absence of divalent ions but is further catalyzed when they are present. After 'feeding' 50 times with activated amino acid in the presence of the Mg2+ ion, oligomers longer than the 20-mer could be detected. The effect of hydroxylapatite on peptide elongation is very sensitive to the nature of the activated amino acid and the acceptor peptide. Glutamic acid oligomerizes more efficiently than L-gamma-carboxyglutamic acid on hydroxylapatite and adds more efficiently to decaglutamic acid in solution. One might, therefore, expect that glutamic acid would add more efficiently than L-gamma-carboxyglutamic acid to decaglutamic acid on hydroxylapatite. The contrary is true--the addition of L-gamma-carboxyglutamic acid is substantially more efficient. This suggests that oligomerization on the surface of hydroxylapatite depends on the detailed match between the structure of the surface of the mineral and the structure of the oligomer.

Chromosome catastrophes involve replication mechanisms generating complex genomic rearrangements

PubMed Central

Liu, Pengfei; Erez, Ayelet; Sreenath Nagamani, Sandesh C.; Dhar, Shweta U.; Kołodziejska, Katarzyna E.; Dharmadhikari, Avinash V.; Cooper, M. Lance; Wiszniewska, Joanna; Zhang, Feng; Withers, Marjorie A.; Bacino, Carlos A.; Campos-Acevedo, Luis Daniel; Delgado, Mauricio R.; Freedenberg, Debra; Garnica, Adolfo; Grebe, Theresa A.; Hernández-Almaguer, Dolores; Immken, LaDonna; Lalani, Seema R.; McLean, Scott D.; Northrup, Hope; Scaglia, Fernando; Strathearn, Lane; Trapane, Pamela; Kang, Sung-Hae L.; Patel, Ankita; Cheung, Sau Wai; Hastings, P. J.; Stankiewicz, Paweł; Lupski, James R.; Bi, Weimin

2011-01-01

SUMMARY Complex genomic rearrangements (CGR) consisting of two or more breakpoint junctions have been observed in genomic disorders. Recently, a chromosome catastrophe phenomenon termed chromothripsis, in which numerous genomic rearrangements are apparently acquired in one single catastrophic event, was described in multiple cancers. Here we show that constitutionally acquired CGRs share similarities with cancer chromothripsis. In the 17 CGR cases investigated we observed localization and multiple copy number changes including deletions, duplications and/or triplications, as well as extensive translocations and inversions. Genomic rearrangements involved varied in size and complexities; in one case, array comparative genomic hybridization revealed 18 copy number changes. Breakpoint sequencing identified characteristic features, including small templated insertions at breakpoints and microhomology at breakpoint junctions, which have been attributed to replicative processes. The resemblance between CGR and chromothripsis suggests similar mechanistic underpinnings. Such chromosome catastrophic events appear to reflect basic DNA metabolism operative throughout an organism’s life cycle. PMID:21925314

Total synthesis of (+)-achalensolide based on the rh(i)-catalyzed allenic Pauson-Khand-type reaction.

PubMed

Hirose, Toshiyuki; Miyakoshi, Naoki; Mukai, Chisato

2008-02-01

The first total synthesis of (+)-achalensolide was achieved from a commercially available d-(-)-isoascorbic acid. The known epoxide, derived from d-(-)-isoascorbic acid, was converted into the allenyne, the Rh(I)-catalyzed Pauson-Khand-type reaction of which directly provided the bicyclo[5.3.0]decane system, a core framework of the title natural product. The construction of the gamma-lactone moiety and some chemical modifications resulted in the completion of the total synthesis of (+)-achalensolide.

Lipase-catalyzed highly enantioselective kinetic resolution of boron-containing chiral alcohols.

PubMed

Andrade, Leandro H; Barcellos, Thiago

2009-07-16

The first application of enzymes as catalysts to obtain optically pure boron compounds is described. The kinetic resolution of boron-containing chiral alcohols via enantioselective transesterification catalyzed by lipases was studied. Aromatic, allylic, and aliphatic secondary alcohols containing a boronate ester or boronic acid group were resolved by lipase from Candida antartica (CALB), and excellent E values (E > 200) and high enantiomeric excesses (up to >99%) of both remaining substrates and acetylated product were obtained.

Degradation of nitrobenzene by a Pseudomonas pseudoalcaligenes.

PubMed Central

Nishino, S F; Spain, J C

1993-01-01

A Pseudomonas pseudoalcaligenes able to use nitrobenzene as the sole source of carbon, nitrogen, and energy was isolated from soil and groundwater contaminated with nitrobenzene. The range of aromatic substrates able to support growth was limited to nitrobenzene, hydroxylaminobenzene, and 2-aminophenol. Washed suspensions of nitrobenzene-grown cells removed nitrobenzene from culture fluids with the concomitant release of ammonia. Nitrobenzene, nitrosobenzene, hydroxylaminobenzene, and 2-aminophenol stimulated oxygen uptake in resting cells and in extracts of nitrobenzene-grown cells. Under aerobic and anaerobic conditions, crude extracts converted nitrobenzene to 2-aminophenol with oxidation of 2 mol of NADPH. Ring cleavage, which required ferrous iron, produced a transient yellow product with a maximum A380. In the presence of NAD, the product disappeared and NADH was produced. In the absence of NAD, the ring fission product was spontaneously converted to picolinic acid, which was not further metabolized. These results indicate that the catabolic pathway involves the reduction of nitrobenzene to nitrosobenzene and then to hydroxylaminobenzene; each of these steps requires 1 mol of NADPH. An enzyme-mediated Bamberger-like rearrangement converts hydroxylaminobenzene to 2-aminophenol, which then undergoes meta ring cleavage to 2-aminomuconic semialdehyde. The mechanism for release of ammonia and subsequent metabolism are under investigation. PMID:8368838

Kinetics of Ethyl Acetate Synthesis Catalyzed by Acidic Resins

ERIC Educational Resources Information Center

Antunes, Bruno M.; Cardoso, Simao P.; Silva, Carlos M.; Portugal, Ines

2011-01-01

A low-cost experiment to carry out the second-order reversible reaction of acetic acid esterification with ethanol to produce ethyl acetate is presented to illustrate concepts of kinetics and reactor modeling. The reaction is performed in a batch reactor, and the acetic acid concentration is measured by acid-base titration versus time. The…

40 CFR 81.341 - South Carolina.

Code of Federal Regulations, 2012 CFR

2012-07-01

... County X Anderson County X Bamberg County X Barnwell County X Beaufort County X Berkeley County X Calhoun... County X Bamberg County X Barnwell County X Beaufort County X Berkeley County X Calhoun County X... Calhoun County Charleston County Cherokee County Chester County Chesterfield County Clarendon County...

40 CFR 81.341 - South Carolina.

Code of Federal Regulations, 2013 CFR

2013-07-01

... County X Anderson County X Bamberg County X Barnwell County X Beaufort County X Berkeley County X Calhoun... County X Bamberg County X Barnwell County X Beaufort County X Berkeley County X Calhoun County X... Calhoun County Charleston County Cherokee County Chester County Chesterfield County Clarendon County...

Chromosomal Rainbows detect Oncogenic Rearrangements of Signaling Molecules in Thyroid Tumors

DOE Office of Scientific and Technical Information (OSTI.GOV)

O'Brien, Benjamin; Jossart, Gregg H.; Ito, Yuko

2010-08-19

Altered signal transduction can be considered a hallmark of many solid tumors. In thyroid cancers the receptor tyrosine kinase (rtk) genes NTRK1 (Online Mendelian Inheritance in Man = OMIM *191315, also known as 'TRKA'), RET ('Rearranged during Transfection protooncogene', OMIM *164761) and MET (OMIM *164860) have been reported as activated, rearranged or overexpressed. In many cases, a combination of cytogenetic and molecular techniques allows elucidation of cellular changes that initiate tumor development and progression. While the mechanisms leading to overexpression of the rtk MET gene remain largely unknown, a variety of chromosomal rearrangements of the RET or NTKR1 gene couldmore » be demonstrated in thyroid cancer. Abnormal expressions in these tumors seem to follow a similar pattern: the rearrangement translocates the 3'-end of the rtk gene including the entire catalytic domain to an expressed gene leading to a chimeric RNA and protein with kinase activity. Our research was prompted by an increasing number of reports describing translocations involving ret and previously unknown translocation partners. We developed a high resolution technique based on fluorescence in situ hybridization (FISH) to allow rapid screening for cytogenetic rearrangements which complements conventional chromosome banding analysis. Our technique applies simultaneous hybridization of numerous probes labeled with different reporter molecules which are distributed along the target chromosome allowing the detection of cytogenetic changes at near megabase-pair (Mbp) resolution. Here, we report our results using a probe set specific for human chromosome 10, which is altered in a significant portion of human thyroid cancers (TC's). While rendering accurate information about the cytogenetic location of rearranged elements, our multi-locus, multi-color analysis was developed primarily to overcome limitations of whole chromosome painting (WCP) and chromosome banding techniques for fine

Chemo- and regioselective homogeneous rhodium-catalyzed hydroamidomethylation of terminal alkenes to N-alkylamides.

PubMed

Raoufmoghaddam, Saeed; Drent, Eite; Bouwman, Elisabeth

2013-09-01

A rhodium/xantphos homogeneous catalyst system has been developed for direct chemo- and regioselective mono-N-alkylation of primary amides with 1-alkenes and syngas through catalytic hydroamidomethylation with 1-pentene and acetamide as model substrates. For appropriate catalyst performance, it appears to be essential that catalytic amounts of a strong acid promoter, such as p-toluenesulfonic acid (HOTs), as well as larger amounts of a weakly acidic protic promoter, particularly hexafluoroisopropyl alcohol (HOR(F) ) are applied. Apart from the product N-1-hexylacetamide, the isomeric unsaturated intermediates, hexanol and higher mass byproducts, as well as the corresponding isomeric branched products, can be formed. Under optimized conditions, almost full alkene conversion can be achieved with more than 80% selectivity to the product N-1-hexylamide. Interestingly, in the presence of a relatively high concentration of HOR(F) , the same catalyst system shows a remarkably high selectivity for the formation of hexanol from 1-pentene with syngas, thus presenting a unique example of a selective rhodium-catalyzed hydroformylation-hydrogenation tandem reaction under mild conditions. Time-dependent product formation during hydroamidomethylation batch experiments provides evidence for aldehyde and unsaturated intermediates; this clearly indicates the three-step hydroformylation/condensation/hydrogenation reaction sequence that takes place in hydroamidomethylation. One likely role of the weakly acidic protic promoter, HOR(F) , in combination with the strong acid HOTs, is to establish a dual-functionality rhodium catalyst system comprised of a neutral rhodium(I) hydroformylation catalyst species and a cationic rhodium(III) complex capable of selectively reducing the imide and/or ene-amide intermediates that are in a dynamic, acid-catalyzed condensation equilibrium with the aldehyde and amide in a syngas environment. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Interception of the Enzymatic Conversion of Farnesyl Diphosphate to 5-Epi-Aristolochene by Using a Fluoro Substrate Analogue: 1-Fluorogermacrene A from (2E,6Z)-6-Fluorofarnesyl Diphosphate**

PubMed Central

Faraldos, Juan A.; Zhao, Yuxin; O'Maille, Paul E.; Noel, Joseph P.; Coates, Robert M.

2009-01-01

Tobacco 5-epi-aristolochene synthase (TEAS) catalyzes the MgII-dependent cyclizations and rearrangements of (E,E)-farnesyl diphosphate (PP) to the bicyclic sesquiterpene hydrocarbon via a tightly bound (+)-germacrene A as a deprotonated intermediate. With the native enzyme, only a few percent of the putative germacrene A intermediate is released from the active site during the catalytic cycle. 6-Fluorofarnesyl PP was designed and synthesized with the aim of arresting the cyclization-rearrangement mechanism en route to 5-epi-aristolochene. Indeed, incubation of (2E,6Z)-6-fluorofarnesyl PP with recombinant TEAS afforded (-)-1-fluororogermacrene A as the sole product in 58% yield. Steady-state kinetic experiments with farnesyl PP and the 6-fluoro analogue showed that the overall catalytic efficiencies (kcat/Km) are essentially the same for both substrates. 1-Fluorogermacrene A was characterized by chromatographic properties (TLC, GC), MS, optical rotation, UV, IR and 1H NMR data, and by heat-induced Cope rearrangement to (+)-1-fluoro-β-elemene. 1H NMR spectra at room temperature revealed that this (E,E)-configured fluorocyclodecadiene exists in solution as a 7:3 mixture of UU and UD conformers. 1-Fluorogermacrene A underwent trifluoroacetic acid-catalyzed cyclization to give three 1α-fluoroselinene isomers at a rate estimated to be about 1000 times slower than that of the similar cyclization of (+)-germacrene A to the parent selinenes. PMID:17886322

Palladium-catalyzed hydroaminocarbonylation of alkenes with amines: a strategy to overcome the basicity barrier imparted by aliphatic amines.

PubMed

Zhang, Guoying; Gao, Bao; Huang, Hanmin

2015-06-22

A novel and efficient palladium-catalyzed hydroaminocarbonylation of alkenes with aminals has been developed under mild reaction conditions, and allows the synthesis of a wide range of N-alkyl linear amides in good yields with high regioselectivity. On the basis of this method, a cooperative catalytic system operating by the synergistic combination of palladium, paraformaldehyde, and acid was established for promoting the hydroaminocarbonylation of alkenes with both aromatic and aliphatic amines, which do not react well under conventional palladium-catalyzed hydroaminocarbonylation. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Oligomerization of glycine and alanine catalyzed by iron oxides: implications for prebiotic chemistry.

PubMed

Shanker, Uma; Bhushan, Brij; Bhattacharjee, G; Kamaluddin

2012-02-01

Iron oxide minerals are probable constituents of the sediments present in geothermal regions of the primitive earth. They might have adsorbed different organic monomers (amino acids, nucleotides etc.) and catalyzed polymerization processes leading to the formation of the first living cell. In the present work we tested the catalytic activity of three forms of iron oxides (Goethite, Akaganeite and Hematite) in the intermolecular condensation of each of the amino acids glycine and L-alanine. The effect of zinc oxide and titanium dioxide on the oligomerization has also been studied. Oligomerization studies were performed for 35 days at three different temperatures 50, 90 and 120°C without applying drying/wetting cycling. The products formed were characterized by HPLC and ESI-MS techniques. All three forms of iron oxides catalyzed peptide bond formation (23.2% of gly2 and 10.65% of ala2). The reaction was monitored every 7 days. Formation of peptides was observed to start after 7 days at 50°C. Maximum yield of peptides was found after 35 days at 90°C. Reaction at 120°C favors formation of diketopiperazine derivatives. It is also important to note that after 35 days of reaction, goethite produced dimer and trimer with the highest yield among the oxides tested. We suggest that the activity of goethite could probably be due to its high surface area and surface acidity.

NHC-catalyzed cleavage of vicinal diketones and triketones followed by insertion of enones and ynones.

PubMed

Takaki, Ken; Hino, Makoto; Ohno, Akira; Komeyama, Kimihiro; Yoshida, Hiroto; Fukuoka, Hiroshi

2017-01-01

Thiazolium carbene-catalyzed reactions of 1,2-diketones and 1,2,3-triketones with enones and ynones have been investigated. The diketones gave α,β-double acylation products via unique Breslow intermediates isolable as acid salts, whereas the triketones formed stable adducts with the NHC instead of the coupling products.

EqualTDRL: illustrating equivalent tandem duplication random loss rearrangements.

PubMed

Hartmann, Tom; Bernt, Matthias; Middendorf, Martin

2018-05-30

To study the differences between two unichromosomal circular genomes, e.g., mitochondrial genomes, under the tandem duplication random loss (TDRL) rearrangement it is important to consider the whole set of potential TDRL rearrangement events that could have taken place. The reason is that for two given circular gene orders there can exist different TDRL rearrangements that transform one of the gene orders into the other. Hence, a TDRL event cannot always be reconstructed only from the knowledge of the circular gene order before a TDRL event and the circular gene order after it. We present the program EqualTDRL that computes and illustrates the complete set of TDRLs for pairs of circular gene orders that differ by only one TDRL. EqualTDRL considers the circularity of the given genomes and certain restrictions on the TDRL rearrangements. Examples for the latter are sequences of genes that have to be conserved during a TDRL or pairs of genes that frame intergenic regions which might represent remnants of duplicated genes. Additionally, EqualTDRL allows to determine the set of TDRLs that are minimum with respect to the number of duplicated genes. EqualTDRL supports scientists to study the complete set of TDRLs that possibly could have taken place in the evolution of mitochondrial genomes. EqualTDRL is implemented in C++ using the ggplot2 package of the open source programming language R and is freely available from http://pacosy.informatik.uni-leipzig.de/equaltdrl .

Microbial degradation of poly(amino acid)s.

PubMed

Obst, Martin; Steinbüchel, Alexander

2004-01-01

Natural poly(amino acid)s are a group of poly(ionic) molecules (ionomers) with various biological functions and putative technical applications and play, therefore, an important role both in nature and in human life. Because of their biocompatibility and their synthesis from renewable resources, poly(amino acid)s may be employed for many different purposes covering a broad spectrum of medical, pharmaceutical, and personal care applications as well as the domains of agriculture and of environmental applications. Biodegradability is one important advantage of naturally occurring poly(amino acid)s over many synthetic polymers. The intention of this review is to give an overview about the enzyme systems catalyzing the initial steps in poly(amino acid) degradation. The focus is on the naturally occurring poly(amino acid)s cyanophycin, poly(epsilon-L-lysine) and poly(gamma-glutamic acid); but biodegradation of structurally related synthetic polyamides such as poly(aspartic acid) and nylons, which are known from various technical applications, is also included.

A Complex 6p25 Rearrangement in a Child With Multiple Epiphyseal Dysplasia

PubMed Central

Bedoyan, Jirair K.; Lesperance, Marci M.; Ackley, Todd; Iyer, Ramaswamy K.; Innis, Jeffrey W.; Misra, Vinod K.

2015-01-01

Genomic rearrangements are increasingly recognized as important contributors to human disease. Here we report on an 11½-year-old child with myopia, Duane retraction syndrome, bilateral mixed hearing loss, skeletal anomalies including multiple epiphyseal dysplasia, and global developmental delay, and a complex 6p25 genomic rearrangement. We have employed oligonucleotide-based comparative genomic hybridization arrays (aCGH) of different resolutions (44 and 244K) as well as a 1 M single nucleotide polymorphism (SNP) array to analyze this complex rearrangement. Our analyses reveal a complex rearrangement involving a ~2.21 Mb interstitial deletion, a ~240 kb terminal deletion, and a 70–80 kb region in between these two deletions that shows maintenance of genomic copy number. The interstitial deletion contains eight known genes, including three Forkhead box containing (FOX) transcription factors (FOXQ1, FOXF2, and FOXC1). The region maintaining genomic copy number partly overlaps the dual specificity protein phosphatase 22 (DUSP22) gene. Array analyses suggest a homozygous loss of genomic material at the 5′ end of DUSP22, which was corroborated using TaqMan® copy number analysis. It is possible that this homozygous genomic loss may render both copies of DUSP22 or its products non-functional. Our analysis suggests a rearrangement mechanism distinct from a previously reported replication-based error-prone mechanism without template switching for a specific 6p25 rearrangement with a 1.22 Mb interstitial deletion. Our study demonstrates the utility and limitations of using oligonucleotide-based aCGH and SNP array technologies of increasing resolutions in order to identify complex DNA rearrangements and gene disruptions. PMID:21204225

NHC-catalyzed cleavage of vicinal diketones and triketones followed by insertion of enones and ynones

PubMed Central

Hino, Makoto; Ohno, Akira; Komeyama, Kimihiro; Yoshida, Hiroto; Fukuoka, Hiroshi

2017-01-01

Thiazolium carbene-catalyzed reactions of 1,2-diketones and 1,2,3-triketones with enones and ynones have been investigated. The diketones gave α,β-double acylation products via unique Breslow intermediates isolable as acid salts, whereas the triketones formed stable adducts with the NHC instead of the coupling products. PMID:28904625

[Ru/AC catalyzed ozonation of recalcitrant organic compounds].

PubMed

Wang, Jian-Bing; Hou, Shao-Pei; Zhou, Yun-Rui; Zhu, Wan-Peng; He, Xu-Wen

2009-09-15

Ozonation and Ru/AC catalyzed ozonation of dimethyl phthalate (DMP), phenols and disinfection by-products precursors were studied. It shows that Ru/AC catalyst can obviously enhance the mineralization of organic compounds. In the degradation of DMP, TOC removal was 28.84% by ozonation alone while it was 66.13% by catalytic ozonation. In the oxidation of 23 kinds of phenols, TOC removals were 9.57%-56.08% by ozonation alone while they were 41.81%-82.32% by catalytic ozonation. Compared to ozonation alone, Ru/AC catalyzed ozonation was more effective for the reduction of disinfection by-products formation potentials in source water. The reduction of haloacetic acids formation potentials was more obvious than thichlomethane formation potentials. After the treatment by catalytic ozonation, the haloacetic acids formation potentials decreased from 144.02 microg/L to 58.50 microg/L, which was below the standard value of EPA. However ozonation alone could not make it reach the standard. The treatments of source water by BAC, O3 + BAC, O3/AC + BAC and Ru/AC + O3 + BAC were also studied. In the four processes, TOC removal was 3.80%, 20.14%, 27.45% and 48.30% respectively, COD removal was 4.37%, 27.22%, 39.91% and 50.00% respectively, UV254 removal was 8.16%, 62.24%, 67.03% and 84.95% respectively. Ru/AC + O3 + BAC process is more effective than the other processes for the removal of TOC, COD and UV254 and no ruthenium leaching observed in the solution. It is a promising process for the treatment of micro polluted source water.

Transformation of follicular lymphoma to plasmablastic lymphoma with c-myc gene rearrangement.

PubMed

Ouansafi, Ihsane; He, Bing; Fraser, Cory; Nie, Kui; Mathew, Susan; Bhanji, Rumina; Hoda, Rana; Arabadjief, Melissa; Knowles, Daniel; Cerutti, Andrea; Orazi, Attilio; Tam, Wayne

2010-12-01

Follicular lymphoma (FL) is an indolent lymphoma that transforms to high-grade lymphoma, mostly diffuse large B-cell lymphoma, in about a third of patients. We present the first report of a case of FL that transformed to plasmablastic lymphoma (PBL). Clonal transformation of the FL to PBL was evidenced by identical IGH/BCL2 gene rearrangements and VDJ gene usage in rearranged IGH genes. IGH/ BCL2 translocation was retained in the PBL, which also acquired c-myc gene rearrangement. Genealogic analysis based on somatic hypermutation of the rearranged IGH genes of both FL and PBL suggests that transformation of the FL to PBL occurred most likely by divergent evolution from a common progenitor cell rather than direct evolution from the FL clone. Our study of this unusual case expands the histologic spectrum of FL transformation and increases our understanding of the pathogenetic mechanisms of transformation of indolent lymphomas to aggressive lymphomas.

The Manifestation of Chromosome Rearrangements in Unordered Asci of Neurospora

PubMed Central

Perkins, David D.

1974-01-01

Rapid, effective techniques have been developed for detecting and characterizing chromosome aberrations in Neurospora by visual inspection of ascospores and asci. Rearrangements that are detectable by the presence of deficient, nonblack ascospores in test crosses make up 5 to 10% of survivors after UV doses giving 10-55% survival. Over 135 rearrangements have been diagnosed by classifying unordered asci according to numbers of defective spores. (These include 15 originally identified or analyzed by other workers.) About 100 reciprocal translocations (RT's) have been confirmed and mapped genetically, involving all combinations of the seven chromosomes. Thirty-three other rearrangements generate viable nontandem duplications in meiosis. These consist of insertional translocations (IT's) (15 confirmed), and of rearrangements that involve a chromosome tip (10 translocations and 3 pericentric inversions). No inversion has been found that does not include the centromere. A reciprocal translocation was found within one population in nature. When pairs of RT's that involve the same two chromosome arms were intercrossed, viable duplications were produced if the breakpoints overlapped in such a way that pairing resembled that of insertional translocations (27 combinations).—The rapid analytical technique depends on the following. Deficiency ascospores are usually nonblack (W: "white") and inviable, while nondeficient ascospores, even those that include duplications, are black (B) and viable. Thus RT's typically produce 50% black spores, and IT's 75% black. Asci are shot spontaneously from ripe perithecia, and can be collected in large numbers as groups of eight ascospores representing unordered tetrads, which fall into five classes: 8B:0W; 6B:2W, 4B:4W, 2B:6B, 0B:8W. In isosequential crosses, 90-95% of tetrads are 8:0. When a rearrangement is heterozygous, the frequencies of tetrad classes are diagnostic of the type of rearrangement, and provide information also on the

Mechanistic Insights from Reaction of α-Oxiranyl-Aldehydes with Cyanobacterial Aldehyde Deformylating Oxygenase

PubMed Central

Das, Debasis; Ellington, Benjamin; Paul, Bishwajit; Marsh, E. Neil G.

2014-01-01

The biosynthesis of long-chain aliphatic hydrocarbons, which are derived from fatty acids, is widespread in Nature. The last step in this pathway involves the decarbonylation of fatty aldehydes to the corresponding alkanes or alkenes. In cyanobacteria this is catalyzed by an aldehyde deformylating oxygenase. We have investigated the mechanism of this enzyme using substrates bearing an oxirane ring adjacent to the aldehyde carbon. The enzyme catalyzed the deformylation of these substrates to produce the corresponding oxiranes. Performing the reaction in D2O allowed the facial selectivity of proton addition to be examined by 1H-NMR spectroscopy. The proton is delivered with equal probability to either face of the oxirane ring, indicating the formation of an oxiranyl radical intermediate that is free to rotate during the reaction. Unexpectedly, the enzyme also catalyzes a side reaction in which oxiranyl-aldehydes undergo tandem deformylation to furnish alkanes two carbons shorter. We present evidence that this involves the rearrangement of the intermediate oxiranyl radical formed in the first step, resulting an aldehyde that is further deformylated in a second step. These observations provide support for a radical mechanism for deformylation and, furthermore, allow the lifetime of the radical intermediate to be estimated based on prior measurements of rate constants for the rearrangement of oxiranyl radicals. PMID:24313866

DNA-Catalyzed Amide Hydrolysis.

PubMed

Zhou, Cong; Avins, Joshua L; Klauser, Paul C; Brandsen, Benjamin M; Lee, Yujeong; Silverman, Scott K

2016-02-24

DNA catalysts (deoxyribozymes) for a variety of reactions have been identified by in vitro selection. However, for certain reactions this identification has not been achieved. One important example is DNA-catalyzed amide hydrolysis, for which a previous selection experiment instead led to DNA-catalyzed DNA phosphodiester hydrolysis. Subsequent efforts in which the selection strategy deliberately avoided phosphodiester hydrolysis led to DNA-catalyzed ester and aromatic amide hydrolysis, but aliphatic amide hydrolysis has been elusive. In the present study, we show that including modified nucleotides that bear protein-like functional groups (any one of primary amino, carboxyl, or primary hydroxyl) enables identification of amide-hydrolyzing deoxyribozymes. In one case, the same deoxyribozyme sequence without the modifications still retains substantial catalytic activity. Overall, these findings establish the utility of introducing protein-like functional groups into deoxyribozymes for identifying new catalytic function. The results also suggest the longer-term feasibility of deoxyribozymes as artificial proteases.

Iodine-Catalyzed Isomerization of Dimethyl Muconate.

PubMed

Settle, Amy E; Berstis, Laura; Zhang, Shuting; Rorrer, Nicholas A; Hu, Haiming; Richards, Ryan M; Beckham, Gregg T; Crowley, Michael F; Vardon, Derek R

2018-06-11

cis,cis-Muconic acid is a platform bio-based chemical that can be upgraded to drop-in commodity and novel monomers. Among the possible drop-in products, dimethyl terephthalate can be synthesized via esterification, isomerization, Diels-Alder cycloaddition, and dehydrogenation. The isomerization of cis,cis-dimethyl muconate (ccDMM) to the trans,trans-form (ttDMM) can be catalyzed by iodine; however, studies have yet to address (i) the mechanism and reaction barriers unique to DMM, and (ii) the influence of solvent, potential for catalyst recycle, and recovery of high-purity ttDMM. To address this gap, we apply a joint computational and experimental approach to investigate iodine-catalyzed isomerization of DMM. Density functional theory calculations identified unique regiochemical considerations owing to the large number of halogen-diene coordination schemes. Both transition state theory and experiments estimate significant barrier reductions with photodissociated iodine. Solvent selection was critical for rapid kinetics, likely because of solvent complexation with iodine. Under select conditions, ttDMM yields of 95 % were achieved in <1 h with methanol, followed by high purity recovery (>98 %) with crystallization. Lastly, post-reaction iodine can be recovered and recycled with minimal loss of activity. Overall, these findings provide new insight into the mechanism and conditions necessary for DMM isomerization with iodine to advance the state-of-the-art for bio-based chemicals. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Chromosomal Rearrangements as Barriers to Genetic Homogenization between Archaic and Modern Humans

PubMed Central

Rogers, Rebekah L.

2015-01-01

Chromosomal rearrangements, which shuffle DNA throughout the genome, are an important source of divergence across taxa. Using a paired-end read approach with Illumina sequence data for archaic humans, I identify changes in genome structure that occurred recently in human evolution. Hundreds of rearrangements indicate genomic trafficking between the sex chromosomes and autosomes, raising the possibility of sex-specific changes. Additionally, genes adjacent to genome structure changes in Neanderthals are associated with testis-specific expression, consistent with evolutionary theory that new genes commonly form with expression in the testes. I identify one case of new-gene creation through transposition from the Y chromosome to chromosome 10 that combines the 5′-end of the testis-specific gene Fank1 with previously untranscribed sequence. This new transcript experienced copy number expansion in archaic genomes, indicating rapid genomic change. Among rearrangements identified in Neanderthals, 13% are transposition of selfish genetic elements, whereas 32% appear to be ectopic exchange between repeats. In Denisovan, the pattern is similar but numbers are significantly higher with 18% of rearrangements reflecting transposition and 40% ectopic exchange between distantly related repeats. There is an excess of divergent rearrangements relative to polymorphism in Denisovan, which might result from nonuniform rates of mutation, possibly reflecting a burst of transposable element activity in the lineage that led to Denisovan. Finally, loci containing genome structure changes show diminished rates of introgression from Neanderthals into modern humans, consistent with the hypothesis that rearrangements serve as barriers to gene flow during hybridization. Together, these results suggest that this previously unidentified source of genomic variation has important biological consequences in human evolution. PMID:26399483

"Does college alcohol consumption impact employment upon graduation? Findings from a prospective study": Correction to Bamberger et al. (2017).

PubMed

2018-01-01

Reports an error in "Does College Alcohol Consumption Impact Employment Upon Graduation? Findings From a Prospective Study" by Peter A. Bamberger, Jaclyn Koopmann, Mo Wang, Mary Larimer, Inbal Nahum-Shani, Irene Geisner and Samuel B. Bacharach ( Journal of Applied Psychology , Advanced Online Publication, Aug 24, 2017, np). In the article, the authors incorrectly used the term "probability" instead of the term "odds" when relating to the impact of drinking in college on post-graduation employment. The abstract should note "a roughly 10% reduction in the odds...", and in the 2nd paragraph of the Discussion section, (a) "a roughly 10% lower probability" should be "a roughly 10% lower odds", and (b) "their probability of full-time employment upon graduation is roughly 6% lower than..." should be "their odds of full-time employment upon graduation is roughly 6% lower than..." All versions of this article have been corrected. (The following abstract of the original article appeared in record 2017-36105-001.) Although scholars have extensively studied the impact of academic and vocational factors on college students' employment upon graduation, we still know little as to how students' health-related behaviors influence such outcomes. Focusing on student alcohol use as a widely prevalent, health-related behavior, in the current study, we examined the employment implications of student drinking behavior. Drawing from literature examining the productivity effects of drinking and research on job search, we posited that modal quantity and frequency of alcohol consumption, as well as the frequency of heavy episodic drinking (HED) adversely impact the probability of employment upon graduation. Using data from 827 graduating seniors from 4 geographically diverse universities in the United States collected in the context of a prospective study design, we found modal alcohol consumption to have no adverse effect on the likelihood of employment upon graduation. However, we did find

Detection of circulating tumor cells harboring a unique ALK rearrangement in ALK-positive non-small-cell lung cancer.

PubMed

Pailler, Emma; Adam, Julien; Barthélémy, Amélie; Oulhen, Marianne; Auger, Nathalie; Valent, Alexander; Borget, Isabelle; Planchard, David; Taylor, Melissa; André, Fabrice; Soria, Jean Charles; Vielh, Philippe; Besse, Benjamin; Farace, Françoise

2013-06-20

The diagnostic test for ALK rearrangement in non-small-cell lung cancer (NSCLC) for crizotinib treatment is currently done on tumor biopsies or fine-needle aspirations. We evaluated whether ALK rearrangement diagnosis could be performed by using circulating tumor cells (CTCs). The presence of an ALK rearrangement was examined in CTCs of 18 ALK-positive and 14 ALK-negative patients by using a filtration enrichment technique and filter-adapted fluorescent in situ hybridization (FA-FISH), a FISH method optimized for filters. ALK-rearrangement patterns were determined in CTCs and compared with those present in tumor biopsies. ALK-rearranged CTCs and tumor specimens were characterized for epithelial (cytokeratins, E-cadherin) and mesenchymal (vimentin, N-cadherin) marker expression. ALK-rearranged CTCs were monitored in five patients treated with crizotinib. All ALK-positive patients had four or more ALK-rearranged CTCs per 1 mL of blood (median, nine CTCs per 1 mL; range, four to 34 CTCs per 1 mL). No or only one ALK-rearranged CTC (median, one per 1 mL; range, zero to one per 1 mL) was detected in ALK-negative patients. ALK-rearranged CTCs harbored a unique (3'5') split pattern, and heterogeneous patterns (3'5', only 3') of splits were present in tumors. ALK-rearranged CTCs expressed a mesenchymal phenotype contrasting with heterogeneous epithelial and mesenchymal marker expressions in tumors. Variations in ALK-rearranged CTC levels were detected in patients being treated with crizotinib. ALK rearrangement can be detected in CTCs of patients with ALK-positive NSCLC by using a filtration technique and FA-FISH, enabling both diagnostic testing and monitoring of crizotinib treatment. Our results suggest that CTCs harboring a unique ALK rearrangement and mesenchymal phenotype may arise from clonal selection of tumor cells that have acquired the potential to drive metastatic progression of ALK-positive NSCLC.

Engineering entropy-driven reactions and networks catalyzed by DNA.

PubMed

Zhang, David Yu; Turberfield, Andrew J; Yurke, Bernard; Winfree, Erik

2007-11-16

Artificial biochemical circuits are likely to play as large a role in biological engineering as electrical circuits have played in the engineering of electromechanical devices. Toward that end, nucleic acids provide a designable substrate for the regulation of biochemical reactions. However, it has been difficult to incorporate signal amplification components. We introduce a design strategy that allows a specified input oligonucleotide to catalyze the release of a specified output oligonucleotide, which in turn can serve as a catalyst for other reactions. This reaction, which is driven forward by the configurational entropy of the released molecule, provides an amplifying circuit element that is simple, fast, modular, composable, and robust. We have constructed and characterized several circuits that amplify nucleic acid signals, including a feedforward cascade with quadratic kinetics and a positive feedback circuit with exponential growth kinetics.

Anaerobic mineralization of quaternary carbon atoms: isolation of denitrifying bacteria on pivalic acid (2,2-dimethylpropionic acid).

PubMed

Probian, Christina; Wülfing, Annika; Harder, Jens

2003-03-01

The degradability of pivalic acid was established by the isolation of several facultative denitrifying strains belonging to Zoogloea resiniphila, to Thauera and Herbaspirillum, and to Comamonadaceae, related to [Aquaspirillum] and Acidovorax, and of a nitrate-reducing bacterium affiliated with Moraxella osloensis. Pivalic acid was completely mineralized to carbon dioxide. The catabolic pathways may involve an oxidation to dimethylmalonate or a carbon skeleton rearrangement, a putative 2,2-dimethylpropionyl coenzyme A mutase.

An active site rearrangement within the Tetrahymena group I ribozyme releases nonproductive interactions and allows formation of catalytic interactions

PubMed Central

Sengupta, Raghuvir N.; Van Schie, Sabine N.S.; Giambaşu, George; Dai, Qing; Yesselman, Joseph D.; York, Darrin; Piccirilli, Joseph A.; Herschlag, Daniel

2016-01-01

Biological catalysis hinges on the precise structural integrity of an active site that binds and transforms its substrates and meeting this requirement presents a unique challenge for RNA enzymes. Functional RNAs, including ribozymes, fold into their active conformations within rugged energy landscapes that often contain misfolded conformers. Here we uncover and characterize one such “off-pathway” species within an active site after overall folding of the ribozyme is complete. The Tetrahymena group I ribozyme (E) catalyzes cleavage of an oligonucleotide substrate (S) by an exogenous guanosine (G) cofactor. We tested whether specific catalytic interactions with G are present in the preceding E•S•G and E•G ground-state complexes. We monitored interactions with G via the effects of 2′- and 3′-deoxy (–H) and −amino (–NH2) substitutions on G binding. These and prior results reveal that G is bound in an inactive configuration within E•G, with the nucleophilic 3′-OH making a nonproductive interaction with an active site metal ion termed MA and with the adjacent 2′-OH making no interaction. Upon S binding, a rearrangement occurs that allows both –OH groups to contact a different active site metal ion, termed MC, to make what are likely to be their catalytic interactions. The reactive phosphoryl group on S promotes this change, presumably by repositioning the metal ions with respect to G. This conformational transition demonstrates local rearrangements within an otherwise folded RNA, underscoring RNA's difficulty in specifying a unique conformation and highlighting Nature's potential to use local transitions of RNA in complex function. PMID:26567314

An active site rearrangement within the Tetrahymena group I ribozyme releases nonproductive interactions and allows formation of catalytic interactions.

PubMed

Sengupta, Raghuvir N; Van Schie, Sabine N S; Giambaşu, George; Dai, Qing; Yesselman, Joseph D; York, Darrin; Piccirilli, Joseph A; Herschlag, Daniel

2016-01-01

Biological catalysis hinges on the precise structural integrity of an active site that binds and transforms its substrates and meeting this requirement presents a unique challenge for RNA enzymes. Functional RNAs, including ribozymes, fold into their active conformations within rugged energy landscapes that often contain misfolded conformers. Here we uncover and characterize one such "off-pathway" species within an active site after overall folding of the ribozyme is complete. The Tetrahymena group I ribozyme (E) catalyzes cleavage of an oligonucleotide substrate (S) by an exogenous guanosine (G) cofactor. We tested whether specific catalytic interactions with G are present in the preceding E•S•G and E•G ground-state complexes. We monitored interactions with G via the effects of 2'- and 3'-deoxy (-H) and -amino (-NH(2)) substitutions on G binding. These and prior results reveal that G is bound in an inactive configuration within E•G, with the nucleophilic 3'-OH making a nonproductive interaction with an active site metal ion termed MA and with the adjacent 2'-OH making no interaction. Upon S binding, a rearrangement occurs that allows both -OH groups to contact a different active site metal ion, termed M(C), to make what are likely to be their catalytic interactions. The reactive phosphoryl group on S promotes this change, presumably by repositioning the metal ions with respect to G. This conformational transition demonstrates local rearrangements within an otherwise folded RNA, underscoring RNA's difficulty in specifying a unique conformation and highlighting Nature's potential to use local transitions of RNA in complex function. © 2015 Sengupta et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Quantitative and Qualitative Changes in V-J α Rearrangements During Mouse Thymocytes Differentiation

PubMed Central

Pasqual, Nicolas; Gallagher, Maighréad; Aude-Garcia, Catherine; Loiodice, Mélanie; Thuderoz, Florence; Demongeot, Jacques; Ceredig, Rod; Marche, Patrice Noël; Jouvin-Marche, Evelyne

2002-01-01

Knowledge of the complete nucleotide sequence of the mouse TCRAD locus allows an accurate determination V-J rearrangement status. Using multiplex genomic PCR assays and real time PCR analysis, we report a comprehensive and systematic analysis of the V-J recombination of TCR α chain in normal mouse thymocytes during development. These respective qualitative and quantitative approaches give rise to four major points describing the control of gene rearrangements. (a) The V-J recombination pattern is not random during ontogeny and generates a limited TCR α repertoire; (b) V-J rearrangement control is intrinsic to the thymus; (c) each V gene rearranges to a set of contiguous J segments with a gaussian-like frequency; (d) there are more rearrangements involving V genes at the 3′ side than 5′ end of V region. Taken together, this reflects a preferential association of V and J gene segments according to their respective positions in the locus, indicating that accessibility of both V and J regions is coordinately regulated, but in different ways. These results provide a new insight into TCR α repertoire size and suggest a scenario for V usage during differentiation. PMID:12417627

Titanium-Beta Zeolites Catalyze the Stereospecific Isomerization of D-Glucose to L-Sorbose via Intramolecular C5-C1 Hydride Shift

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gounder, Rajamani; Davis, Mark E.

Pure-silica zeolite beta containing Lewis acidic framework Ti 4+ centers (Ti-Beta) is shown to catalyze the isomerization of D-glucose to L-sorbose via an intramolecular C5–C1 hydride shift. Glucose–sorbose isomerization occurs in parallel to glucose–fructose isomerization on Ti-Beta in both water and methanol solvents, with fructose formed as the predominant product in water and sorbose as the predominant product in methanol (at 373 K) at initial times and over the course of >10 turnovers. Isotopic tracer studies demonstrate that 13C and D labels placed respectively at the C1 and C2 positions of glucose are retained respectively at the C6 and C5more » positions of sorbose, consistent with its formation via an intramolecular C5–C1 hydride shift isomerization mechanism. This direct Lewis acid-mediated pathway for glucose–sorbose isomerization appears to be unprecedented among heterogeneous or biological catalysts and sharply contrasts indirect base-mediated glucose–sorbose isomerization via 3,4-enediol intermediates or via retro-aldol fragmentation and recombination of sugar fragments. Measured first-order glucose–sorbose isomerization rate constants (per total Ti; 373 K) for Ti-Beta in methanol are similar for glucose and glucose deuterated at the C2 position (within a factor of ~1.1), but are a factor of ~2.3 lower for glucose deuterated at each carbon position, leading to H/D kinetic isotope effects expected for kinetically relevant intramolecular C5–C1 hydride shift steps. Optical rotation measurements show that isomerization of D-(+)-glucose (92% enantiomeric purity) with Ti-Beta in water (373 K) led to the formation of L-(-)-sorbose (73% enantiomeric purity) and D-(-)-fructose (87% enantiomeric purity) as the predominant stereoisomers, indicating that stereochemistry is preserved at carbon centers not directly involved in intramolecular C5–C1 or C2–C1 hydride shift steps, respectively. This new Lewis acid-mediated rearrangement of glucose

Soft Ultraviolet (UV) Photopatterning and Metallization of Self-Assembled Monolayers (SAMs) Formed from the Lipoic Acid Ester of α-Hydroxy-1-acetylpyrene: The Generality of Acid-Catalyzed Removal of Thiol-on-Gold SAMs using Soft UV Light.

PubMed

Pukenas, Laurynas; Prompinit, Panida; Nishitha, Boda; Tate, Daniel J; Singh, N D Pradeep; Wälti, Christoph; Evans, Stephen D; Bushby, Richard J

2017-05-31

Under a layer of 0.1 M HCl in isopropanol, soft ultraviolet (UV) (365 nm) photolysis of the thiol-on-gold self-assembled monolayer (SAM) derived from the lipoic acid ester of α-hydroxy-1-acetylpyrene results in the expected removal of the acetylpyrene protecting group. When photolyzing through a mask, this can be used to produce a patterned surface and, at a controlled electrochemical potential, it is then possible to selectively and reversibly electrodeposit copper on the photolyzed regions. Rather surprisingly, under these photolysis conditions, there is not only the expected photodeprotection of the ester but also partial removal of the lipoic acid layer which has been formed. In further studies, it is shown that this type of acid-catalyzed photoremoval of SAM layers by soft UV is a rather general phenomenon and results in the partial removal of the thiol-on-gold SAM layers derived from other ω-thiolated carboxylic acids. However, this phenomenon is chain-length dependent. Under conditions in which there is a ∼60% reduction in the thickness of the SAM derived from dithiobutyric acid, the SAM derived from mercaptoundecanoic acid is almost unaffected. The process by which the shorter-chain SAM layers are partially removed is not fully understood because these compounds do not absorb significantly in the 365 nm region of the spectrum! Significantly, this study shows that acid catalysis photolysis of thiol-on-gold SAMs needs to be used with caution.

High level of chromosomal instability in circulating tumor cells of ROS1-rearranged non-small-cell lung cancer.

PubMed

Pailler, E; Auger, N; Lindsay, C R; Vielh, P; Islas-Morris-Hernandez, A; Borget, I; Ngo-Camus, M; Planchard, D; Soria, J-C; Besse, B; Farace, F

2015-07-01

Genetic aberrations affecting the c-ros oncogene 1 (ROS1) tyrosine kinase gene have been reported in a small subset of patients with non-small-cell lung cancer (NSCLC). We evaluated whether ROS1-chromosomal rearrangements could be detected in circulating tumor cells (CTCs) and examined tumor heterogeneity of CTCs and tumor biopsies in ROS1-rearranged NSCLC patients. Using isolation by size of epithelial tumor cells (ISET) filtration and filter-adapted-fluorescence in situ hybridization (FA-FISH), ROS1 rearrangement was examined in CTCs from four ROS1-rearranged patients treated with the ROS1-inhibitor, crizotinib, and four ROS1-negative patients. ROS1-gene alterations observed in CTCs at baseline from ROS1-rearranged patients were compared with those present in tumor biopsies and in CTCs during crizotinib treatment. Numerical chromosomal instability (CIN) of CTCs was assessed by DNA content quantification and chromosome enumeration. ROS1 rearrangement was detected in the CTCs of all four patients with ROS1 rearrangement previously confirmed by tumor biopsy. In ROS1-rearranged patients, median number of ROS1-rearranged CTCs at baseline was 34.5 per 3 ml blood (range, 24-55). In ROS1-negative patients, median background hybridization of ROS1-rearranged CTCs was 7.5 per 3 ml blood (range, 7-11). Tumor heterogeneity, assessed by ROS1 copy number, was significantly higher in baseline CTCs compared with paired tumor biopsies in the three patients experiencing PR or SD (P < 0.0001). Copy number in ROS1-rearranged CTCs increased significantly in two patients who progressed during crizotinib treatment (P < 0.02). CTCs from ROS1-rearranged patients had a high DNA content and gain of chromosomes, indicating high levels of aneuploidy and numerical CIN. We provide the first proof-of-concept that CTCs can be used for noninvasive and sensitive detection of ROS1 rearrangement in NSCLC patients. CTCs from ROS1-rearranged patients show considerable heterogeneity of ROS1-gene

High level of chromosomal instability in circulating tumor cells of ROS1-rearranged non-small-cell lung cancer

PubMed Central

Pailler, E.; Auger, N.; Lindsay, C. R.; Vielh, P.; Islas-Morris-Hernandez, A.; Borget, I.; Ngo-Camus, M.; Planchard, D.; Soria, J.-C.; Besse, B.; Farace, F.

2015-01-01

Background Genetic aberrations affecting the c-ros oncogene 1 (ROS1) tyrosine kinase gene have been reported in a small subset of patients with non-small-cell lung cancer (NSCLC). We evaluated whether ROS1-chromosomal rearrangements could be detected in circulating tumor cells (CTCs) and examined tumor heterogeneity of CTCs and tumor biopsies in ROS1-rearranged NSCLC patients. Patients and methods Using isolation by size of epithelial tumor cells (ISET) filtration and filter-adapted-fluorescence in situ hybridization (FA-FISH), ROS1 rearrangement was examined in CTCs from four ROS1-rearranged patients treated with the ROS1-inhibitor, crizotinib, and four ROS1-negative patients. ROS1-gene alterations observed in CTCs at baseline from ROS1-rearranged patients were compared with those present in tumor biopsies and in CTCs during crizotinib treatment. Numerical chromosomal instability (CIN) of CTCs was assessed by DNA content quantification and chromosome enumeration. Results ROS1 rearrangement was detected in the CTCs of all four patients with ROS1 rearrangement previously confirmed by tumor biopsy. In ROS1-rearranged patients, median number of ROS1-rearranged CTCs at baseline was 34.5 per 3 ml blood (range, 24–55). In ROS1-negative patients, median background hybridization of ROS1-rearranged CTCs was 7.5 per 3 ml blood (range, 7–11). Tumor heterogeneity, assessed by ROS1 copy number, was significantly higher in baseline CTCs compared with paired tumor biopsies in the three patients experiencing PR or SD (P < 0.0001). Copy number in ROS1-rearranged CTCs increased significantly in two patients who progressed during crizotinib treatment (P < 0.02). CTCs from ROS1-rearranged patients had a high DNA content and gain of chromosomes, indicating high levels of aneuploidy and numerical CIN. Conclusion We provide the first proof-of-concept that CTCs can be used for noninvasive and sensitive detection of ROS1 rearrangement in NSCLC patients. CTCs from ROS1-rearranged

Inhibitors of amino acids biosynthesis as antifungal agents.

PubMed

Jastrzębowska, Kamila; Gabriel, Iwona

2015-02-01

Fungal microorganisms, including the human pathogenic yeast and filamentous fungi, are able to synthesize all proteinogenic amino acids, including nine that are essential for humans. A number of enzymes catalyzing particular steps of human-essential amino acid biosynthesis are fungi specific. Numerous studies have shown that auxotrophic mutants of human pathogenic fungi impaired in biosynthesis of particular amino acids exhibit growth defect or at least reduced virulence under in vivo conditions. Several chemical compounds inhibiting activity of one of these enzymes exhibit good antifungal in vitro activity in minimal growth media, which is not always confirmed under in vivo conditions. This article provides a comprehensive overview of the present knowledge on pathways of amino acids biosynthesis in fungi, with a special emphasis put on enzymes catalyzing particular steps of these pathways as potential targets for antifungal chemotherapy.

Spliceostatin hemiketal biosynthesis in Burkholderia spp. is catalyzed by an iron/α-ketoglutarate–dependent dioxygenase

PubMed Central

Eustáquio, Alessandra S.; Janso, Jeffrey E.; Ratnayake, Anokha S.; O’Donnell, Christopher J.; Koehn, Frank E.

2014-01-01

Spliceostatins are potent spliceosome inhibitors biosynthesized by a hybrid nonribosomal peptide synthetase−polyketide synthase (NRPS−PKS) system of the trans-acyl transferase (AT) type. Burkholderia sp. FERM BP-3421 produces hemiketal spliceostatins, such as FR901464, as well as analogs containing a terminal carboxylic acid. We provide genetic and biochemical evidence for hemiketal biosynthesis by oxidative decarboxylation rather than the previously hypothesized Baeyer–Villiger oxidative release postulated to be catalyzed by a flavin-dependent monooxygenase (FMO) activity internal to the last module of the PKS. Inactivation of Fe(II)/α-ketoglutarate–dependent dioxygenase gene fr9P led to loss of hemiketal congeners, whereas the mutant was still able to produce all major carboxylic acid-type compounds. FMO mutants, on the other hand, produced both hemiketal and carboxylic acid analogs containing an exocyclic methylene instead of an epoxide, indicating that the FMO is involved in epoxidation rather than Baeyer–Villiger oxidation. Moreover, recombinant Fr9P enzyme was shown to catalyze hydroxylation to form β-hydroxy acids, which upon decarboxylation led to hemiketal FR901464. Finally, a third oxygenase activity encoded in the biosynthetic gene cluster, the cytochrome P450 monooxygenase Fr9R, was assigned as a 4-hydroxylase based on gene inactivation results. Identification and deletion of the gene involved in hemiketal formation allowed us to generate a strain—the dioxygenase fr9P− mutant—that accumulates only the carboxylic acid-type spliceostatins, which are as potent as the hemiketal analogs, when derivatized to increase cell permeability, but are chemically more stable. PMID:25097259

Enhancement effects of chelating agents on the degradation of tetrachloroethene in Fe(III) catalyzed percarbonate system

PubMed Central

Miao, Zhouwei; Gu, Xiaogang; Lu, Shuguang; Brusseau, Mark L.; Zhang, Xiang; Fu, Xiaori; Danish, Muhammad; Qiu, Zhaofu; Sui, Qian

2015-01-01

The performance of Fe(III)-based catalyzed sodium percarbonate (SPC) for stimulating the oxidation of tetrachloroethene (PCE) for groundwater remediation applications was investigated. The chelating agents citric acid monohydrate (CIT), oxalic acid (OA), and Glutamic acid (Glu) significantly enhanced the degradation of PCE. Conversely, ethylenediaminetetraacetic acid (EDTA) had a negative impact on PCE degradation, which may due to its strong Fe chelation and HO• scavenging abilities. However, excessive SPC or chelating agent will retard PCE degradation. In addition, investigations using free radical probe compounds and radical scavengers revealed that PCE was primarily degraded by HO• radical oxidation in both the chelated and non-chelated systems, while O2•− also participated in the non-chelated system and the OA and Glu modified systems. According to the electron paramagnetic resonance (EPR) studies, the presence of HO• in the Fe(III)/SPC system was maintained much longer than that in the Fe(II)/SPC system. The results indicated that the addition of CIT, OA or Glu indeed enhanced the generation of HO• in the first 10 min and promoted degradation efficiency by increasing the amount of Fe(III) and maintaining the concentration of HO• radicals in solution. In conclusion, chelated Fe(III)-based catalyzed SPC oxidation is a promising method for the remediation of PCE-contaminated groundwater. PMID:26549979

Chemo-enzymatic synthesis of furfuralcohol from chestnut shell hydrolysate by a sequential acid-catalyzed dehydration under microwave and Escherichia coli CCZU-Y10 whole-cells conversion.

PubMed

Di, Junhua; Ma, Cuiluan; Qian, Jianghao; Liao, Xiaolong; Peng, Bo; He, Yucai

2018-08-01

In this study, chemo-enzymatic synthesis of furfuralcohol from biomass-derived xylose was successfully demonstrated by a sequential acid-catalyzed dehydration under microwave and whole-cells reduction. After dry dewaxed chestnut shells (CNS, 75 g/L) was acid-hydrolyzed with dilute oxalic acid (0.5 wt%) at 140 °C for 40 min, the obtained CNS-derived xylose (17.9 g/L xylose) could be converted to furfural at 78.8% yield with solid acid SO 4 2- /SnO 2 -Attapulgite (2.0 wt% catalyst loading) in the dibutyl phthalate-water (1:1, v:v) under microwave (600 W) at 180 °C for 10 min. In the dibutyl phthalate-water (1:1, v/v) media at 30 °C and pH 6.5, the furfural liquor (47.0 mM furfural) was biologically converted to furfuralcohol by recombinant Escherichia coli CCZU-Y10 whole-cells harboring an NADH-dependent reductase (PgCR) without extra addition of NAD + and glucose, and furfural was completely converted to furfuralcohol after 2.5 h. Clearly, this one-pot synthesis strategy can be effectively used for furfuralcohol production. Copyright © 2018 Elsevier Ltd. All rights reserved.

Thermo-kinetics of lipase-catalyzed synthesis of 6-O-glucosyldecanoate.

PubMed

Gumel, A M; Annuar, M S M; Heidelberg, T; Chisti, Y

2011-10-01

Lipase-catalyzed synthesis of 6-O-glucosyldecanoate from d-glucose and decanoic acid was performed in dimethyl sulfoxide (DMSO), a mixture of DMSO and tert-butanol and tert-butanol alone with a decreasing order of polarity. The highest conversion yield (> 65%) of decanoic acid was obtained in the blended solvent of intermediate polarity mainly because it could dissolve relatively large amounts of both the reactants. The reaction obeyed Michaelis-Menten type of kinetics. The affinity of the enzyme towards the limiting substrate (decanoic acid) was not affected by the polarity of the solvent, but increased significantly with temperature. The esterification reaction was endothermic with activation energy in the range of 60-67 kJ mol⁻¹. Based on the Gibbs energy values, in the solvent blend of DMSO and tert-butanol the position of the equilibrium was shifted more towards the products compared to the position in pure solvents. Monoester of glucose was the main product of the reaction. Copyright © 2011 Elsevier Ltd. All rights reserved.

Imino-Oxy Acetic Acid Dealkylation as Evidence for an Inner-Sphere Alcohol Intermediate in the Reaction Catalyzed by Peptidylglycine α-Hydroxylating Monooxygenase (PHM)

PubMed Central

McIntyre, Neil R.; Lowe, Edward W.; Merkler, David J.

2009-01-01

Peptidylglycine α-hydroxylating monooxygenase (PHM, EC 1.14.17.3) catalyzes the stereospecific hydroxylation of a glycyl α-carbon in a reaction that requires O2 and ascorbate. Subsequent dealkylation of the α-hydroxyglycine by another enzyme, peptidylamidoglycolate lyase (PAL. EC 4.3.2.5), yields a bioactive amide and glyoxylate. PHM is a non-coupled, type II dicopper monooxygenase which activates O2 at only a single copper atom, CuM. In this study, the PHM mechanism was probed using a non-natural substrate, benzaldehyde imino-oxy acetic acid (BIAA). PHM catalyzes the O-oxidative dealkylation of BIAA to benzaldoxime and glyoxylate with no involvement of PAL. The minimal kinetic mechanism for BIAA was shown to be steady-state ordered using primary deuterium kinetic isotope effects. The D(V/K)APPARENT, BIAA decreased from 14.7 ± 1.0 as [O2] → 0 to 1.0 ± 0.2 as [O2] → ∞ suggesting the dissociation rate constant from the PHM·BIAA complex decreases as [O2] increases; thereby, reducing the steady-state concentration of [PHM]free. BIAA was further used to differentiate between potential oxidative Cu/O species using a QM/MM reaction coordinate simulation to determine which species could yield product O-dealkylation that matched our experimental data. The results of this study provided compelling evidence for the presence of a covalently linked CuII-alkoxide intermediate with a quartet spin state responsible BIAA oxidation. PMID:19569683

Ionic Liquid Catalyzed Electrolyte for Electrochemical Polyaniline Supercapacitors

NASA Astrophysics Data System (ADS)

Inamdar, A. I.; Im, Hyunsik; Jung, Woong; Kim, Hyungsang; Kim, Byungchul; Yu, Kook-Hyun; Kim, Jin-Sang; Hwang, Sung-Min

2013-05-01

The effect of different wt.% of ionic liquid "1,6-bis (trimethylammonium-1-yl) hexane tetrafluoroborate" in 0.5 M LiClO4+PC electrolyte on the supercapacitor properties of polyaniline (PANI) thin film are investigated. The PANI film is synthesized using electropolymerization of aniline in the presence of sulfuric acid. The electrochemical properties of the PANI thin film are studied by cyclic voltammetry, galvanostatic charge-discharge and electrochemical impedance spectroscopy (EIS) measurements. The optimum amount of the ionic liquid is found to be 2 wt.% which provides better ionic conductivity of the electrolyte. The highest specific capacitance of 259 F/g is obtained using the 2 wt.% electrolyte. This capacitance remains at up to 208 F/g (80% capacity retention) after 1000 charge-discharge cycles at a current density of 0.5 mA/g. The PANI film in the 2 wt.% ionic liquid catalyzed 0.5 M LiClO4+PC electrolyte shows small electrochemical resistance, better rate performance and higher cyclability. The increased ionic conductivity of the 2 wt.% ionic liquid catalyzed electrolyte causes a reduction in resistance at the electrode/electrolyte interface, which can be useful in electrochemically-preferred power devices for better applicability.

Fe0 catalyzed photo-Fenton process to detoxify the biodegraded products of azo dye Mordant Yellow 10.

PubMed

Brindha, R; Muthuselvam, P; Senthilkumar, S; Rajaguru, P

2018-06-01

Inspired by the efficiency of the photo-Fenton process on oxidation of organic pollutants, we herein present the feasibility of visible light driven photo-Fenton process as a post treatment of biological method for the effective degradation and detoxification of monoazo dye Mordant Yellow 10 (MY10). Anaerobic degradation of MY10 by Pseudomonas aeroginosa formed aromatic amines which were further degraded in the subsequent Fe catalyzed photo-Fenton process carried out at pH 3.0, with iron shavings and H 2 O 2 under blue LED light illumination. LC-MS and stoichiometric analysis confirmed that reductive azo bond cleavage was the major reaction in anaerobic bacterial degradation of MY10 producing 4-amino benzene sulfonic acid (4-ABS) and 5-amino salicylic acid (5-ASA) which were further degraded into hydroxyl amines, nitroso and di/tri carboxylic acids by the photo-Fenton process. Toxicity studies with human small cell lung cancer A549 cells provide evidence that incorporation of Fe 0 catalyzed photo-Fenton step after anaerobic bacterial treatment improved the mineralization and detoxification of MY10 dye. Copyright © 2018 Elsevier Ltd. All rights reserved.

Copper-catalyzed C(sp3)-OH cleavage with concomitant C-C coupling: synthesis of 3-substituted isoindolinones.

PubMed

Rao, H Surya Prakash; Rao, A Veera Bhadra

2015-02-06

Copper(II) trifluoromethanesulfonate (Cu(OTf)2) efficiently catalyzes the C-C coupling of 3-hydoxyisoindolinones with a variety of aryl-, heteroaryl-, and alkenylboronic acids to furnish C(3) aryl-, heteroaryl-, and alkenyl-substituted isoindolinones. The coupling reactions work smoothly in 1,2-dicholoroethane (DCE) reflux, to effect both inter- and intramolecular versions. This is the first report on C(sp(3))-OH cleavage with concomitant C-C coupling. The photolabile 2-nitrobenzyl protecting group is most appropriate for promotion of the coupling reaction and for deprotection. The tetracyclic ring motif of the alkaloid neuvamine was prepared by applying the newly developed copper-catalyzed C-C coupling.

Nickel-Catalyzed, Carbonyl-Ene-Type Reactions: Selective for Alpha Olefins and More Efficient with Electron-Rich Aldehydes

PubMed Central

Ho, Chun-Yu; Ng, Sze-Sze; Jamison, Timothy F.

2011-01-01

Described are several classes of unusual or unprecedented carbonyl-ene-type reactions, including those between alpha olefins and aromatic aldehydes. Catalyzed by nickel, these processes complement existing Lewis acid-catalyzed methods in several respects. Not only are monosubstituted alkenes, aromatic aldehydes, and tert-alkyl aldehydes effective substrates, but monosubstituted olefins also react faster than those that are more substituted, and large or electron-rich aldehydes are more effective than small or electron-poor ones. Conceptually, in the presence of a nickel-phosphine catalyst, the combination of off-the-shelf alkenes, silyl triflates, and triethylamine functions as a replacement for an allylmetal reagent. PMID:16620106

Major pathologic response to alectinib in ALK-rearranged adenocarcinoma of the lung.

PubMed

Imanishi, Naoko; Yoneda, Kazue; Taira, Akihiro; Ichiki, Yoshinobu; Sato, Naoko; Hisaoka, Masanori; Tanaka, Fumihiro

2018-03-09

Alectinib is a highly selective tyrosine kinase inhibitor of anaplastic lymphoma kinase (ALK) and provided a significantly prolonged progression-free survival compared with chemotherapy in patients with advanced non-small cell lung cancer (NSCLC) harboring rearrangements of the ALK gene. Here, we present the first surgical case of ALK-rearranged lung adenocarcinoma with major pathological response in resected specimens after treatment with alectinib. A 65-year-old female with clinical stage IIIA-N2 ALK-rearranged adenocarcinoma originating from the left lower lobe presented. Involvement of lower para-tracheal node was pathologically confirmed by endobronchial ultrasound-guided biopsy. Alectinib was prescribed, as the patient may not tolerate radiotherapy due to a mental illness. After 3 months' treatment with alectinib, a remarkable radiological and metabolic response was achieved. The patient did not tolerate further continuation of alectinib treatment, and surgery was performed without any morbidity. Only < 10% tumor cells were viable in all resected specimens, indicating major pathological response to alectinib. Salvage surgery after alectinib treatment may be safe and effective for initially unresectable NSCLC harboring ALK-rearrangements.

Clinical features of squamous cell lung cancer with anaplastic lymphoma kinase (ALK)-rearrangement: a retrospective analysis and review

PubMed Central

Watanabe, Junko; Togo, Shinsaku; Sumiyoshi, Issei; Namba, Yukiko; Suina, Kentaro; Mizuno, Takafumi; Kadoya, Kotaro; Motomura, Hiroaki; Iwai, Moe; Nagaoka, Tetsutaro; Sasaki, Shinichi; Hayashi, Takuo; Uekusa, Toshimasa; Abe, Kanae; Urata, Yasuo; Sakurai, Fuminori; Mizuguchi, Hiroyuki; Kato, Shunsuke; Takahashi, Kazuhisa

2018-01-01

Anti-anaplastic lymphoma kinase (ALK)-targeted therapy dramatically improves therapeutic responses in patients with ALK-rearranged lung adenocarcinoma (Ad-LC). A few cases of squamous cell lung carcinoma (Sq-LC) with ALK rearrangement have been reported; however, the clinicopathological features and clinical outcomes following treatment with ALK inhibitors are unknown. We addressed this in the present study by retrospectively comparing the clinical characteristics of five patients with ALK-rearranged Sq-LC with those of patients with ALK-rearranged Ad-LC and by evaluating representative cases of ALK inhibitor responders and non-responders. The prevalence of ALK rearrangement in Sq-LCs was 1.36%. Progression-free survival (PFS) after initial treatment with crizotinib was significantly shorter in Sq-LC than in Ad-LC with ALK rearrangement (p = 0.033). Two ALK rearrangements assayed by fluorescence in situ hybridization (FISH)-positive/immunohistochemistry-negative cases did not respond to crizotinb, and PFS decreased following alectinib treatment of ALK-rearranged Sq-LC (p = 0.045). A rebiopsy revealed that responders to ceritinib harbored the L1196M mutation, which causes resistance to other ALK inhibitors. However, non-responders were resistant to all ALK inhibitors, despite the presence of ALK rearrangement in FISH-positive circulating tumor cells and circulating free DNA and absence of the ALK inhibitor resistance mutation. These results indicate that ALK inhibitors remain a reasonable therapeutic option for ALK-rearranged Sq-LC patients who have worse outcomes than ALK-rearranged Ad-LC patients and that resistance mechanisms are heterogeneous. Additionally, oncologists should be aware of the possibility of ALK-rearranged Sq-LC based on clinicopathological features, and plan second-line therapeutic strategies based on rebiopsy results in order to improve patient outcome. PMID:29844868

Clinical features of squamous cell lung cancer with anaplastic lymphoma kinase (ALK)-rearrangement: a retrospective analysis and review.

PubMed

Watanabe, Junko; Togo, Shinsaku; Sumiyoshi, Issei; Namba, Yukiko; Suina, Kentaro; Mizuno, Takafumi; Kadoya, Kotaro; Motomura, Hiroaki; Iwai, Moe; Nagaoka, Tetsutaro; Sasaki, Shinichi; Hayashi, Takuo; Uekusa, Toshimasa; Abe, Kanae; Urata, Yasuo; Sakurai, Fuminori; Mizuguchi, Hiroyuki; Kato, Shunsuke; Takahashi, Kazuhisa

2018-05-08

Anti-anaplastic lymphoma kinase (ALK)-targeted therapy dramatically improves therapeutic responses in patients with ALK-rearranged lung adenocarcinoma (Ad-LC). A few cases of squamous cell lung carcinoma (Sq-LC) with ALK rearrangement have been reported; however, the clinicopathological features and clinical outcomes following treatment with ALK inhibitors are unknown. We addressed this in the present study by retrospectively comparing the clinical characteristics of five patients with ALK-rearranged Sq-LC with those of patients with ALK-rearranged Ad-LC and by evaluating representative cases of ALK inhibitor responders and non-responders. The prevalence of ALK rearrangement in Sq-LCs was 1.36%. Progression-free survival (PFS) after initial treatment with crizotinib was significantly shorter in Sq-LC than in Ad-LC with ALK rearrangement ( p = 0.033). Two ALK rearrangements assayed by fluorescence in situ hybridization (FISH)-positive/immunohistochemistry-negative cases did not respond to crizotinb, and PFS decreased following alectinib treatment of ALK-rearranged Sq-LC ( p = 0.045). A rebiopsy revealed that responders to ceritinib harbored the L1196M mutation, which causes resistance to other ALK inhibitors. However, non-responders were resistant to all ALK inhibitors, despite the presence of ALK rearrangement in FISH-positive circulating tumor cells and circulating free DNA and absence of the ALK inhibitor resistance mutation. These results indicate that ALK inhibitors remain a reasonable therapeutic option for ALK-rearranged Sq-LC patients who have worse outcomes than ALK-rearranged Ad-LC patients and that resistance mechanisms are heterogeneous. Additionally, oncologists should be aware of the possibility of ALK-rearranged Sq-LC based on clinicopathological features, and plan second-line therapeutic strategies based on rebiopsy results in order to improve patient outcome.

Whey protein isolate with improved film properties through cross-linking catalyzed by small laccase from Streptomyces coelicolor.

PubMed

Quan, Wei; Zhang, Chong; Zheng, Meixia; Lu, Zhaoxin; Lu, Fengxia

2018-08-01

The effects of small laccase (SLAC) from Streptomyces coelicolor on the properties of whey protein isolate (WPI) films were studied. WPI was catalyze by SLAC without phenolic acid assistance. Particle size distribution results showed that some complexes with higher relative molecular weight formed in WPI samples treated with SLAC. The content of α-helixes decreased while those of β-sheets and random coils increased following SLAC treatment according to circular dichroism results. Fourier transform infrared spectral analysis suggested that some conformational changes occurred in WPI following SLAC treatment. Analysis of WPI films prepared by casting after SLAC treatment indicated that their film properties were all improved, including mechanical properties, solubility, water vapor, oxygen and carbon dioxide barrier properties, film color, light transmission, transparency and thermal properties. Compared with that of the control film, some obvious differences in the morphology of the WPI films were observed following SLAC treatment. This report demonstrates that laccase can directly catalyze protein cross-linking, which may be useful to improve the performance of protein films. In this study, SLAC was applied to WPI edible film during the film-making process. The results showed that SLAC can catalyze WPI cross-linking without phenolic acid assistance, and WPI film properties were improved after SLAC treatment. © 2018 Society of Chemical Industry. © 2018 Society of Chemical Industry.

Rhodium-catalyzed chemo-, regio-, and enantioselective addition of 2-pyridones to terminal allenes.

PubMed

Li, Changkun; Kähny, Matthias; Breit, Bernhard

2014-12-08

A rhodium-catalyzed chemo-, regio-, and enantioselective addition of 2-pyridones to terminal allenes to give branched N-allyl 2-pyridones is reported. Preliminary mechanistic studies support the hypothesis that the reaction was initiated from the more acidic 2-hydroxypyridine form, and the initial kinetic O-allylation product was finally converted into the thermodynamically more stable N-allyl 2-pyridones. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Catalysis of the Oligomerization of O-Phospho-Serine, Aspartic Acid, or Glutamic Acid by Cationic Micelles

NASA Technical Reports Server (NTRS)

Bohler, Christof; Hill, Aubrey R., Jr.; Orgel, Leslie E.

1996-01-01

Treatment of relatively concentrated aqueous solutions of 0-phospho-serine (50 mM), aspartic acid (100 mM) or glutamic acid (100 mM) with carbonyldiimidazole leads to the formation of an activated intermediate that oligomerizes efficiently. When the concentration of amino acid is reduced tenfold, few long oligomers can be detected. Positively-charged cetyltrimethyl ammonium bromide micelles concentrate the negatively-charged activated intermediates of the amino acids at their surfaces and catalyze efficient oligomerization even from dilute solutions.

Catalysis of the Oligomerization of O-Phospho-Serine, Aspartic Acid, or Glutamic Acid by Cationic Micelles

NASA Technical Reports Server (NTRS)

Boehler, Christof; Hill, Aubrey R., Jr.; Orgel, Leslie E.

1996-01-01

Treatment of relatively concentrated aqueous solutions of O-phospho-serine (50 mM), aspartic acid (100 mM) or glutamic acid (100 mM) with carbonyldiimidazole leads to the formation of an activated intermediate that oligomerizes efficiently. When the concentration of amino acid is reduced tenfold, few long oligomers can be detected. Positively-charged cetyltrimethyl ammonium bromide micelles concentrate the negatively-charged activated intermediates of the amino acids at their surfaces and catalyze efficient oligomerization even from dilute solutions.

Engineering an ATP-dependent D-Ala:D-Ala ligase for synthesizing amino acid amides from amino acids.

PubMed

Miki, Yuta; Okazaki, Seiji; Asano, Yasuhisa

2017-05-01

We successfully engineered a new enzyme that catalyzes the formation of D-Ala amide (D-AlaNH 2 ) from D-Ala by modifying ATP-dependent D-Ala:D-Ala ligase (EC 6.3.2.4) from Thermus thermophilus, which catalyzes the formation of D-Ala-D-Ala from two molecules of D-Ala. The new enzyme was created by the replacement of the Ser293 residue with acidic amino acids, as it was speculated to bind to the second D-Ala of D-Ala-D-Ala. In addition, a replacement of the position with Glu performed better than that with Asp with regards to specificity for D-AlaNH 2 production. The S293E variant, which was selected as the best enzyme for D-AlaNH 2 production, exhibited an optimal activity at pH 9.0 and 40 °C for D-AlaNH 2 production. The apparent K m values of this variant for D-Ala and NH 3 were 7.35 mM and 1.58 M, respectively. The S293E variant could catalyze the synthesis of 9.3 and 35.7 mM of D-AlaNH 2 from 10 and 50 mM D-Ala and 3 M NH 4 Cl with conversion yields of 93 and 71.4 %, respectively. This is the first report showing the enzymatic formation of amino acid amides from amino acids.

Chromosomal rearrangements maintain a polymorphic supergene controlling butterfly mimicry

PubMed Central

Joron, Mathieu; Frezal, Lise; Jones, Robert T.; Chamberlain, Nicola L.; Lee, Siu F.; Haag, Christoph R.; Whibley, Annabel; Becuwe, Michel; Baxter, Simon W.; Ferguson, Laura; Wilkinson, Paul A.; Salazar, Camilo; Davidson, Claire; Clark, Richard; Quail, Michael A.; Beasley, Helen; Glithero, Rebecca; Lloyd, Christine; Sims, Sarah; Jones, Matthew C.; Rogers, Jane; Jiggins, Chris D.; ffrench-Constant, Richard H.

2013-01-01

Supergenes are tight clusters of loci that facilitate the co-segregation of adaptive variation, providing integrated control of complex adaptive phenotypes1. Polymorphic supergenes, in which specific combinations of traits are maintained within a single population, were first described for ‘pin’ and ‘thrum’ floral types in Primula1 and Fagopyrum2, but classic examples are also found in insect mimicry3–5 and snail morphology6. Understanding the evolutionary mechanisms that generate these co-adapted gene sets, as well as the mode of limiting the production of unfit recombinant forms, remains a substantial challenge7–10. Here we show that individual wing-pattern morphs in the polymorphic mimetic butterfly Heliconius numata are associated with different genomic rearrangements at the supergene locus P. These rearrangements tighten the genetic linkage between at least two colour-pattern loci that are known to recombine in closely related species9–11, with complete suppression of recombination being observed in experimental crosses across a 400-kilobase interval containing at least 18 genes. In natural populations, notable patterns of linkage disequilibrium (LD) are observed across the entire P region. The resulting divergent haplotype clades and inversion breakpoints are found in complete association with wing-pattern morphs. Our results indicate that allelic combinations at known wing-patterning loci have become locked together in a polymorphic rearrangement at the Plocus, forming a supergene that acts as a simple switch between complex adaptive phenotypes found in sympatry. These findings highlight how genomic rearrangements can have a central role in the coexistence of adaptive phenotypes involving several genes acting in concert, by locally limiting recombination and gene flow. PMID:21841803

Nicotinic Acid Metabolism, V. A Cobamide Coenzyme-Dependent Conversion of α-Methyleneglutaric Acid to Dimethylmaleic Acid

PubMed Central

Kung, H. F.; Cederbaum, S.; Tsai, L.; Stadtman, T. C.

1970-01-01

A new B12-coenzyme-dependent isomerization, catalyzed by extracts of a nicotinate-fermenting clostridium, results in the conversion of α-methyleneglutaric acid to dimethylmaleic acid. These two acids are intermediates in the multistep anaerobic process wherein nicotinate is converted, ultimately, to one mole each of propionate, acetate, carbon dioxide, and ammonia. Dimethylmaleic acid reacts in its anhydride form with 2,4-dinitrophenylhydrazine to form N-2′,4′-dinitrophenyl-anilino-3,4-dimethylmaleimide. The characteristic reddish color exhibited by the latter derivative in alkaline solution serves as a convenient quantitative assay for dimethylmaleic acid. Comparison of the 2,4-dinitrophenylhydrazine derivatives of the product of the enzymic reaction and of synthetic dimethylmaleic anhydride showed them to be identical in every respect. PMID:5266166

Gas-phase hydration of glyoxylic acid: Kinetics and atmospheric implications.

PubMed

Liu, Ling; Zhang, Xiuhui; Li, Zesheng; Zhang, Yunhong; Ge, Maofa

2017-11-01

Oxocarboxylic acids are one of the most important organic species found in secondary organic aerosols and can be detected in diverse environments. But the hydration of oxocarboxylic acids in the atmosphere has still not been fully understood. Neglecting the hydration of oxocarboxylic acids in atmospheric models may be one of the most important reasons for the significant discrepancies between field measurements and abundance predictions of atmospheric models for oxocarboxylic acids. In the present paper, glyoxylic acid, as the most abundant oxocarboxylic acids in the atmosphere, has been selected as an example to study whether the hydration process can occur in the atmosphere and what the kinetic process of hydration is. The gas-phase hydration of glyoxylic acid to form the corresponding geminal diol and those catalyzed by atmospheric common substances (water, sulfuric acid and ammonia) have been investigated at the CCSD(T)-F12/cc-pVDZ-F12//M06-2X/6-311++G(3df,3pd) level of theory. The contour map of electron density difference of transition states have been further analyzed. It is indicated that these atmospheric common substances can all catalyze on the hydration to some extent and sulfuric acid is the most effective reducing the Gibbs free energy of activation to 9.48 kcal/mol. The effective rate constants combining the overall rate constants and concentrations of the corresponding catalysts have shown that water and sulfuric acid are both important catalysts and the catalysis of sulfuric acid is the most effective for the gas-phase hydration of glyoxylic acid. This catalyzed processes are potentially effective in coastal regions and polluted regions. Copyright © 2017 Elsevier Ltd. All rights reserved.

Biosynthesis of Germacrene A Carboxylic Acid in Chicory Roots. Demonstration of a Cytochrome P450 (+)-Germacrene A Hydroxylase and NADP+-Dependent Sesquiterpenoid Dehydrogenase(s) Involved in Sesquiterpene Lactone Biosynthesis

PubMed Central

de Kraker, Jan-Willem; Franssen, Maurice C. R.; Dalm, Marcella C. F.; de Groot, Aede; Bouwmeester, Harro J.

2001-01-01

Sprouts of chicory (Cichorium intybus), a vegetable grown in the dark, have a slightly bitter taste associated with the presence of guaianolides, eudesmanolides, and germacranolides. The committed step in the biosynthesis of these compounds is catalyzed by a (+)-germacrene A synthase. Formation of the lactone ring is the postulated next step in biosynthesis of the germacrene-derived sesquiterpene lactones. The present study confirms this hypothesis by isolation of enzyme activities from chicory roots that introduce a carboxylic acid function in the germacrene A isopropenyl side chain, which is necessary for lactone ring formation. (+)-Germacrene A is hydroxylated to germacra-1(10),4,11(13)-trien-12-ol by a cytochrome P450 enzyme, and is subsequently oxidized to germacra-1(10),4,11(13)-trien-12-oic acid by NADP+-dependent dehydrogenase(s). Both oxidized germacrenes were detected as their Cope-rearrangement products elema-1,3,11(13)-trien-12-ol and elema-1,3,11(13)-trien-12-oic acid, respectively. The cyclization products of germacra-1(10),4,11(13)-trien-12-ol, i.e. costol, were also observed. The (+)-germacrene A hydroxylase is inhibited by carbon monoxide (blue-light reversible), has an optimum pH at 8.0, and hydroxylates β-elemene with a modest degree of enantioselectivity. PMID:11299372

Clonal immunoglobulin heavy chain and T-cell receptor γ gene rearrangements in primary gastric lymphoma.

PubMed

Shan, Guo-Dong; Hu, Feng-Ling; Yang, Ming; Chen, Hong-Tan; Chen, Wen-Guo; Wang, Yun-Gui; Chen, Li-Hua; Li, You-Ming; Xu, Guo-Qiang

2013-09-14

To study the diagnostic value of immunoglobulin heavy chain (IgH) and T-cell receptor γ (TCR-γ) gene monoclonal rearrangements in primary gastric lymphoma (PGL). A total of 48 patients with suspected PGL at our hospital were prospectively enrolled in this study from January 2009 to December 2011. The patients were divided into three groups (a PGL group, a gastric linitis plastica group, and a benign gastric ulcer group) based on the pathological results (gastric mucosal specimens obtained by endoscopy or surgery) and follow-up. Endoscopic ultrasonography (EUS) and EUS-guided biopsy were performed in all the patients. The tissue specimens were used for histopathological examination and for IgH and TCR-γ gene rearrangement polymerase chain reaction analyses. EUS and EUS-guided biopsy were successfully performed in all 48 patients. In the PGL group (n = 21), monoclonal IgH gene rearrangements were detected in 14 (66.7%) patients. A positive result for each set of primers was found in 12 (57.1%), 8 (38.1%), and 4 (19.0%) cases using FR1/JH, FR2/JH, and FR3/JH primers, respectively. Overall, 12 (75%) patients with mucosal-associated lymphoid tissue lymphoma (n = 16) and 2 (40%) patients with diffuse large B-cell lymphoma (n = 5) were positive for monoclonal IgH gene rearrangements. No patients in the gastric linitis plastica group (n = 17) and only one (10%) patient in the benign gastric ulcer group (n = 10) were positive for a monoclonal IgH gene rearrangement. No TCR-γ gene monoclonal rearrangements were detected. The sensitivity of monoclonal IgH gene rearrangements was 66.7% for a PGL diagnosis, and the specificity was 96.4%. In the PGL group, 8 (100%) patients with stage IIE PGL (n = 8) and 6 (46.1%) patients with stage IE PGL (n = 13) were positive for monoclonal IgH gene rearrangements. IgH gene rearrangements may be associated with PGL staging and may be useful for the diagnosis of PGL and for differentiating between PGL and gastric linitis plastica.

A general heuristic for genome rearrangement problems.

PubMed

Dias, Ulisses; Galvão, Gustavo Rodrigues; Lintzmayer, Carla Négri; Dias, Zanoni

2014-06-01

In this paper, we present a general heuristic for several problems in the genome rearrangement field. Our heuristic does not solve any problem directly, it is rather used to improve the solutions provided by any non-optimal algorithm that solve them. Therefore, we have implemented several algorithms described in the literature and several algorithms developed by ourselves. As a whole, we implemented 23 algorithms for 9 well known problems in the genome rearrangement field. A total of 13 algorithms were implemented for problems that use the notions of prefix and suffix operations. In addition, we worked on 5 algorithms for the classic problem of sorting by transposition and we conclude the experiments by presenting results for 3 approximation algorithms for the sorting by reversals and transpositions problem and 2 approximation algorithms for the sorting by reversals problem. Another algorithm with better approximation ratio can be found for the last genome rearrangement problem, but it is purely theoretical with no practical implementation. The algorithms we implemented in addition to our heuristic lead to the best practical results in each case. In particular, we were able to improve results on the sorting by transpositions problem, which is a very special case because many efforts have been made to generate algorithms with good results in practice and some of these algorithms provide results that equal the optimum solutions in many cases. Our source codes and benchmarks are freely available upon request from the authors so that it will be easier to compare new approaches against our results.

Internal flow inside droplets within a concentrated emulsion during droplet rearrangement

NASA Astrophysics Data System (ADS)

Leong, Chia Min; Gai, Ya; Tang, Sindy K. Y.

2018-03-01

Droplet microfluidics, in which each droplet serves as a micro-reactor, has found widespread use in high-throughput biochemical screening applications. These droplets are often concentrated at various steps to form a concentrated emulsion. As part of a serial interrogation and sorting process, such concentrated emulsions are typically injected into a tapered channel leading to a constriction that fits one drop at a time for the probing of droplet content in a serial manner. The flow physics inside the droplets under these flow conditions are not well understood but are critical for predicting and controlling the mixing of reagents inside the droplets as reactors. Here we investigate the flow field inside droplets of a concentrated emulsion flowing through a tapered microchannel using micro-particle image velocimetry. The confining geometry of the channel forces the number of rows of drops to reduce by one at specific and uniformly spaced streamwise locations, which are referred to as droplet rearrangement zones. Within each rearrangement zone, the phase-averaged velocity results show that the motion of the droplets involved in the rearrangement process, also known as a T1 event, creates vortical structures inside themselves and their adjacent droplets. These flow structures increase the circulation inside droplets up to 2.5 times the circulation in droplets at the constriction. The structures weaken outside of the rearrangement zones suggesting that the flow patterns created by the T1 process are transient. The time scale of circulation is approximately the same as the time scale of a T1 event. Outside of the rearrangement zones, flow patterns in the droplets are determined by the relative velocity between the continuous and disperse phases.

Understanding the hydrolysis mechanism of ethyl acetate catalyzed by an aqueous molybdocene: a computational chemistry investigation.

PubMed

Tílvez, Elkin; Cárdenas-Jirón, Gloria I; Menéndez, María I; López, Ramón

2015-02-16

A thoroughly mechanistic investigation on the [Cp2Mo(OH)(OH2)](+)-catalyzed hydrolysis of ethyl acetate has been performed using density functional theory methodology together with continuum and discrete-continuum solvation models. The use of explicit water molecules in the PCM-B3LYP/aug-cc-pVTZ (aug-cc-pVTZ-PP for Mo)//PCM-B3LYP/aug-cc-pVDZ (aug-cc-pVDZ-PP for Mo) computations is crucial to show that the intramolecular hydroxo ligand attack is the preferred mechanism in agreement with experimental suggestions. Besides, the most stable intermediate located along this mechanism is analogous to that experimentally reported for the norbornenyl acetate hydrolysis catalyzed by molybdocenes. The three most relevant steps are the formation and cleavage of the tetrahedral intermediate immediately formed after the hydroxo ligand attack and the acetic acid formation, with the second one being the rate-determining step with a Gibbs energy barrier of 36.7 kcal/mol. Among several functionals checked, B3LYP-D3 and M06 give the best agreement with experiment as the rate-determining Gibbs energy barrier obtained only differs 0.2 and 0.7 kcal/mol, respectively, from that derived from the experimental kinetic constant measured at 296.15 K. In both cases, the acetic acid elimination becomes now the rate-determining step of the overall process as it is 0.4 kcal/mol less stable than the tetrahedral intermediate cleavage. Apart from clarifying the identity of the cyclic intermediate and discarding the tetrahedral intermediate formation as the rate-determining step for the mechanism of the acetyl acetate hydrolysis catalyzed by molybdocenes, the small difference in the Gibbs energy barrier found between the acetic acid formation and the tetrahedral intermediate cleavage also uncovers that the rate-determining step could change when studying the reactivity of carboxylic esters other than ethyl acetate substrate specific toward molybdocenes or other transition metal complexes. Therefore

Alu elements mediate large SPG11 gene rearrangements: further spatacsin mutations.

PubMed

Conceição Pereira, Maria; Loureiro, José Leal; Pinto-Basto, Jorge; Brandão, Eva; Margarida Lopes, Ana; Neves, Georgina; Dias, Pureza; Geraldes, Ruth; Martins, Isabel Pavão; Cruz, Vitor Tedim; Kamsteeg, Erik-Jan; Brunner, Han G; Coutinho, Paula; Sequeiros, Jorge; Alonso, Isabel

2012-01-01

Hereditary spastic paraplegias compose a group of neurodegenerative disorders with a large clinical and genetic heterogeneity. Among the autosomal recessive forms, spastic paraplegia type 11 is the most common. To better understand the spastic paraplegia type 11 mutation spectrum, we studied a group of 54 patients with hereditary spastic paraplegia. Mutation screening was performed by PCR amplification of SPG11 coding regions and intron boundaries, followed by sequencing. For the detection of large gene rearrangements, we performed multiplex ligation-dependent probe amplification. We report 13 families with spastic paraplegia type 11 carrying either novel or previously identified mutations. We describe a complex entire SPG11 rearrangement and show that large gene rearrangements are frequent among patients with spastic paraplegia type 11. Moreover, we mapped the deletion breakpoints of three different large SPG11 deletions and provide evidence for Alu microhomology-mediated exon deletion. Our analysis shows that the high number of repeated elements in SPG11 together with the presence of recombination hotspots and the high intrinsic instability of the 15q locus all contribute toward making this genomic region more prone to large gene rearrangements. These findings enlarge the amount of data relating repeated elements with neurodegenerative disorders and highlight their importance in human disease and genome evolution.

Synthesis of antiviral tetrahydrocarbazole derivatives by photochemical and acid-catalyzed C-H functionalization via intermediate peroxides (CHIPS).

PubMed

Gulzar, Naeem; Klussmann, Martin

2014-06-20

The direct functionalization of C-H bonds is an important and long standing goal in organic chemistry. Such transformations can be very powerful in order to streamline synthesis by saving steps, time and material compared to conventional methods that require the introduction and removal of activating or directing groups. Therefore, the functionalization of C-H bonds is also attractive for green chemistry. Under oxidative conditions, two C-H bonds or one C-H and one heteroatom-H bond can be transformed to C-C and C-heteroatom bonds, respectively. Often these oxidative coupling reactions require synthetic oxidants, expensive catalysts or high temperatures. Here, we describe a two-step procedure to functionalize indole derivatives, more specifically tetrahydrocarbazoles, by C-H amination using only elemental oxygen as oxidant. The reaction uses the principle of C-H functionalization via Intermediate PeroxideS (CHIPS). In the first step, a hydroperoxide is generated oxidatively using visible light, a photosensitizer and elemental oxygen. In the second step, the N-nucleophile, an aniline, is introduced by Brønsted-acid catalyzed activation of the hydroperoxide leaving group. The products of the first and second step often precipitate and can be conveniently filtered off. The synthesis of a biologically active compound is shown.

Molecular Innovation in Ciliates with Complex Genome Rearrangements

NASA Astrophysics Data System (ADS)

Neme, R.; Landweber, L. F.

2017-07-01

We study molecular innovation in several ciliate species with unique massive genome rearrangements to understand how a radically distinct genome architecture can shape the process of acquiring new functions, genes and structures.

The Robustness of a Signaling Complex to Domain Rearrangements Facilitates Network Evolution

PubMed Central

Sato, Paloma M.; Yoganathan, Kogulan; Jung, Jae H.; Peisajovich, Sergio G.

2014-01-01

The rearrangement of protein domains is known to have key roles in the evolution of signaling networks and, consequently, is a major tool used to synthetically rewire networks. However, natural mutational events leading to the creation of proteins with novel domain combinations, such as in frame fusions followed by domain loss, retrotranspositions, or translocations, to name a few, often simultaneously replace pre-existing genes. Thus, while proteins with new domain combinations may establish novel network connections, it is not clear how the concomitant deletions are tolerated. We investigated the mechanisms that enable signaling networks to tolerate domain rearrangement-mediated gene replacements. Using as a model system the yeast mitogen activated protein kinase (MAPK)-mediated mating pathway, we analyzed 92 domain-rearrangement events affecting 11 genes. Our results indicate that, while domain rearrangement events that result in the loss of catalytic activities within the signaling complex are not tolerated, domain rearrangements can drastically alter protein interactions without impairing function. This suggests that signaling complexes can maintain function even when some components are recruited to alternative sites within the complex. Furthermore, we also found that the ability of the complex to tolerate changes in interaction partners does not depend on long disordered linkers that often connect domains. Taken together, our results suggest that some signaling complexes are dynamic ensembles with loose spatial constraints that could be easily re-shaped by evolution and, therefore, are ideal targets for cellular engineering. PMID:25490747

Facile and Promising Method for Michael Addition of Indole and Pyrrole to Electron-Deficient trans-β-Nitroolefins Catalyzed by a Hydrogen Bond Donor Catalyst Feist's Acid and Preliminary Study of Antimicrobial Activity

PubMed Central

Al Majid, Abdullah M. A.; Islam, Mohammad Shahidul; Barakat, Assem; Al-Agamy, Mohamed H. M.; Naushad, Mu.

2014-01-01

The importance of cooperative hydrogen-bonding effects has been demonstrated using novel 3-methylenecyclopropane-1,2-dicarboxylic acid (Feist's acid (FA)) as hydrogen bond donor catalysts for the addition of indole and pyrrole to trans-β-nitrostyrene derivatives. Because of the hydrogen bond donor (HBD) ability, Feist's acid (FA) has been introduced as a new class of hydrogen bond donor catalysts for the activation of nitroolefin towards nucleophilic substitution reaction. It has effectively catalyzed the Michael addition of indoles and pyrrole to β-nitroolefins under optimum reaction condition to furnish the corresponding Michael adducts in good to excellent yields (up to 98%). The method is general, atom-economical, convenient, and eco-friendly and could provide excellent yields and regioselectivities. Some newly synthesized compounds were for examined in vitro antimicrobial activity and their preliminary results are reported. PMID:24574906

Improved synthesis of isostearic acid using zeolite catalysts

USDA-ARS?s Scientific Manuscript database

Isostearic acids are unique and important biobased products with superior properties. Unfortunately, they are not widely utilized in industry because they are produced as byproducts from a process called clay-catalyzed oligomerization of tall oil fatty acids. Generally, this clay method results in...

Dynamic kinetic asymmetric transformation (DYKAT) by combined amine- and transition-metal-catalyzed enantioselective cycloisomerization.

PubMed

Zhao, Gui-Ling; Ullah, Farman; Deiana, Luca; Lin, Shuangzheng; Zhang, Qiong; Sun, Junliang; Ibrahem, Ismail; Dziedzic, Pawel; Córdova, Armando

2010-02-01

The first examples of one-pot highly chemo- and enantioselective dynamic kinetic asymmetric transformations (DYKATs) involving alpha,beta-unsaturated aldehydes and propargylated carbon acids are presented. These DYKATs, which proceed by a combination of catalytic iminium activation, enamine activation, and Pd(0)-catalyzed enyne cycloisomerization, give access to functionalized cyclopentenes with up to 99 % ee and can be used for the generation of all-carbon quaternary stereocenters.

Cobalt-catalyzed hydrogenation of esters to alcohols: unexpected reactivity trend indicates ester enolate intermediacy.

PubMed

Srimani, Dipankar; Mukherjee, Arup; Goldberg, Alexander F G; Leitus, Gregory; Diskin-Posner, Yael; Shimon, Linda J W; Ben David, Yehoshoa; Milstein, David

2015-10-12

The atom-efficient and environmentally benign catalytic hydrogenation of carboxylic acid esters to alcohols has been accomplished in recent years mainly with precious-metal-based catalysts, with few exceptions. Presented here is the first cobalt-catalyzed hydrogenation of esters to the corresponding alcohols. Unexpectedly, the evidence indicates the unprecedented involvement of ester enolate intermediates. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Highly efficient Cu(I)-catalyzed oxidation of alcohols to ketones and aldehydes with diaziridinone.

PubMed

Zhu, Yingguang; Zhao, Baoguo; Shi, Yian

2013-03-01

A novel and efficient Cu(I)-catalyzed oxidation of alcohols has been achieved with di-tert-butyldiaziridinone as the oxidant under mild conditions. A wide variety of primary and secondary alcohols with various functional groups can be oxidized to aldehydes and ketones in high yields. The reaction proceeds under neutral conditions making it compatible with acid- or base-sensitive substrates, and it is amenable to gram scale.

Silver-Catalyzed Cyclopropanation of Alkenes Using N-Nosylhydrazones as Diazo Surrogates.

PubMed

Liu, Zhaohong; Zhang, Xinyu; Zanoni, Giuseppe; Bi, Xihe

2017-12-15

An efficient silver-catalyzed [2 + 1] cyclopropanation of sterically hindered internal alkenes with diazo compounds in which room-temperature-decomposable N-nosylhydrazones are used as diazo surrogates is reported. The unexpected unique catalytic activity of silver was ascribed to its dual role as a Lewis acid activating alkene substrates and as a transition metal forming silver carbenoids. A wide range of internal alkenes, including challenging diarylethenes, were suitable for this protocol, thereby affording a variety of cyclopropanes with high efficiency in a stereoselective manner under mild conditions.

An endogenous factor enhances ferulic acid decarboxylation catalyzed by phenolic acid decarboxylase from Candida guilliermondii

PubMed Central

2012-01-01

The gene for a eukaryotic phenolic acid decarboxylase of Candida guilliermondii was cloned, sequenced, and expressed in Escherichia coli for the first time. The structural gene contained an open reading frame of 504 bp, corresponding to 168 amino acids with a calculated molecular mass of 19,828 Da. The deduced amino sequence exhibited low similarity to those of functional phenolic acid decarboxylases previously reported from bacteria with 25-39% identity and to those of PAD1 and FDC1 proteins from Saccharomyces cerevisiae with less than 14% identity. The C. guilliermondii phenolic acid decarboxylase converted the main substrates ferulic acid and p-coumaric acid to the respective corresponding products. Surprisingly, the ultrafiltrate (Mr 10,000-cut-off) of the cell-free extract of C. guilliermondii remarkably activated the ferulic acid decarboxylation by the purified enzyme, whereas it was almost without effect on the p-coumaric acid decarboxylation. Gel-filtration chromatography of the ultrafiltrate suggested that an endogenous amino thiol-like compound with a molecular weight greater than Mr 1,400 was responsible for the activation. PMID:22217315

Delineation of the Caffeine C-8 Oxidation Pathway in Pseudomonas sp. Strain CBB1 via Characterization of a New Trimethyluric Acid Monooxygenase and Genes Involved in Trimethyluric Acid Metabolism

PubMed Central

Mohanty, Sujit Kumar; Yu, Chi-Li; Das, Shuvendu; Louie, Tai Man; Gakhar, Lokesh

2012-01-01

The molecular basis of the ability of bacteria to live on caffeine via the C-8 oxidation pathway is unknown. The first step of this pathway, caffeine to trimethyluric acid (TMU), has been attributed to poorly characterized caffeine oxidases and a novel quinone-dependent caffeine dehydrogenase. Here, we report the detailed characterization of the second enzyme, a novel NADH-dependent trimethyluric acid monooxygenase (TmuM), a flavoprotein that catalyzes the conversion of TMU to 1,3,7-trimethyl-5-hydroxyisourate (TM-HIU). This product spontaneously decomposes to racemic 3,6,8-trimethylallantoin (TMA). TmuM prefers trimethyluric acids and, to a lesser extent, dimethyluric acids as substrates, but it exhibits no activity on uric acid. Homology models of TmuM against uric acid oxidase HpxO (which catalyzes uric acid to 5-hydroxyisourate) reveal a much bigger and hydrophobic cavity to accommodate the larger substrates. Genes involved in the caffeine C-8 oxidation pathway are located in a 25.2-kb genomic DNA fragment of CBB1, including cdhABC (coding for caffeine dehydrogenase) and tmuM (coding for TmuM). Comparison of this gene cluster to the uric acid-metabolizing gene cluster and pathway of Klebsiella pneumoniae revealed two major open reading frames coding for the conversion of TM-HIU to S-(+)-trimethylallantoin [S-(+)-TMA]. The first one, designated tmuH, codes for a putative TM-HIU hydrolase, which catalyzes the conversion of TM-HIU to 3,6,8-trimethyl-2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline (TM-OHCU). The second one, designated tmuD, codes for a putative TM-OHCU decarboxylase which catalyzes the conversion of TM-OHCU to S-(+)-TMA. Based on a combination of enzymology and gene-analysis, a new degradative pathway for caffeine has been proposed via TMU, TM-HIU, TM-OHCU to S-(+)-TMA. PMID:22609920

Coupled-rearrangement-channels calculation of the three-body system under the absorbing boundary condition

NASA Astrophysics Data System (ADS)

Iwasaki, M.; Otani, R.; Ito, M.; Kamimura, M.

2016-05-01

We formulate the method of the absorbing boundary condition (ABC) in the coupled-rearrangement-channels variational method (CRCMV) for the three-body problem. In the present study, we handle the simple three-boson system, and the absorbing potential is introduced in the Jacobi coordinate in the individual rearrangement channels. The resonance parameters and the strength of the monopole breakup are compared with the complex scaling method (CSM). We have found that the CRCVM + ABC method nicely works in the threebody problem with the rearrangement channels.

Diazo compounds and N-tosylhydrazones: novel cross-coupling partners in transition-metal-catalyzed reactions.

PubMed

Xiao, Qing; Zhang, Yan; Wang, Jianbo

2013-02-19

Transition-metal-catalyzed carbene transformations and cross-couplings represent two major reaction types in organometallic chemistry and organic synthesis. However, for a long period of time, these two important areas have evolved separately, with essentially no overlap or integration. Thus, an intriguing question has emerged: can cross-coupling and metal carbene transformations be merged into a single reaction cycle? Such a combination could facilitate the development of novel carbon-carbon bond-forming methodologies. Although this concept was first explored about 10 years ago, rapid developments inthis area have been achieved recently. Palladium catalysts can be used to couple diazo compounds with a wide variety of organic halides. Under oxidative coupling conditions, diazo compounds can also react with arylboronic acids and terminal alkynes. Both of these coupling reactions form carbon-carbon double bonds. As the key step in these catalytic processes, Pd carbene migratory insertion plays a vital role in merging the elementary steps of Pd intermediates, leading to novel carbon-carbon bond formations. Because the diazo substrates can be generated in situ from N-tosylhydrazones in the presence of base, the N-tosylhydrazones can be used as reaction partners, making this type of cross-coupling reaction practical in organic synthesis. N-Tosylhydrazones are easily derived from the corresponding aldehydes or ketones. The Pd-catalyzed cross-coupling of N-tosylhydrazones is considered a complementary reaction to the classic Shapiro reaction for converting carbonyl functionalities into carbon-carbon double bonds. It can also serve as an alternative approach for the Pd-catalyzed cross-coupling of carbonyl compounds, which is usually achieved via triflates. The combination of carbene formation and cross-coupling in a single catalytic cycle is not limited to Pd-catalyzed reactions. Recent studies of Cu-, Rh-, Ni-, and Co-catalyzed cross-coupling reactions with diazo

Detection of choline and phosphatidic acid (PA) catalyzed by phospholipase D (PLD) using MALDI-QIT-TOF/MS with 9-aminoacridine matrix.

PubMed

Park, Kyung-Eui; Kim, Jun-Dal; Nagashima, Yusuke; Kako, Koichiro; Daitoku, Hiroaki; Matsui, Motoki; Park, Gwi Gun; Fukamizu, Akiyoshi

2014-01-01

Phospholipase D (PLD) catalyzes the hydrolysis of phosphatidylcholine (PC), the most abundant phospholipids of plasma membrane, resulting in the production of choline and phosphatidic acid (PA). Choline is a precursor of the neurotransmitter acetylcholine, whereas PA functions as an intracellular lipid mediator of diverse biological functions. For assessing PLD activity in vitro, PLD-derived choline has been often analyzed with radioactive or non-radioactive methods. In this study, we have developed a new method for detecting choline and PA with MALDI-QIT-TOF/MS by using 9-aminoacridine as a matrix. The standard calibration curves showed that choline and PA could be detected with linearity over the range from 0.05 and 1 pmol, respectively. Importantly, this method enables the concomitant detection of choline and PA as a reaction product of PC hydrolysis by PLD2 proteins. Thus, our simple and direct method would be useful to characterize the enzymatic properties of PLD, thereby providing insight into mechanisms of PLD activation.

Synthesis of δ- and α-Carbolines via Nickel-Catalyzed [2 + 2 + 2] Cycloaddition of Functionalized Alkyne-Nitriles with Alkynes.

PubMed

Wang, Gaonan; You, Xu; Gan, Yi; Liu, Yuanhong

2017-01-06

A new method for the synthesis of δ- and α-carbolines through Ni-catalyzed [2 + 2 + 2] cycloaddition of ynamide-nitriles or alkyne-cyanamides with alkynes has been developed. The catalytic system of NiCl 2 (DME)/dppp/Zn with a low-cost Ni(II)-precursor was first utilized in Ni-catalyzed [2 + 2 + 2] cycloaddition reactions, and the in situ generated Lewis acid may play an important role for the successful transformation. Not only internal alkynes but also terminal alkynes undergo the desired cycloaddition reactions efficiently to furnish the carboline derivatives with wide diversity and functional group tolerance.

Lysophosphatidylcholine synthesis by lipase-catalyzed ethanolysis.

PubMed

Yang, Guolong; Yang, Ruoxi; Hu, Jingbo

2015-01-01

Lysophosphatidylcholine (LPC) is amphiphilic substance, and possesses excellent physiological functions. In this study, LPC was prepared through ethanolysis of phosphatidylcholine (PC) in n-hexane or solvent free media catalyzed by Novozym 435 (from Candida antarctica), Lipozyme TLIM (from Thermomcyces lanuginosus) and Lipozyme RMIM (from Rhizomucor miehei). The results showed that three immobilized lipases from Candida Antarctica, Thermomcyces lanuginosus and Rhizomucor miehei could catalyze ethanolysis of PC efficiently. In n-hexane, the LPC conversions of ethanolysis of PC catalyzed by Novozyme 435, Lipozyme TLIM and Lipozyme RMIM could reach to 98.5 ± 1.6%, 94.6 ± 1.4% and 93.7 ± 1.8%, respectively. In solvent free media, the highest LPC conversions of ethanolysis of PC catalyzed by Novozyme 435, Lipozyme TL IM and Lipozyme RM IM were 97.7 ± 1.7%, 93.5 ± 1.2% and 93.8 ± 1.9%, respectively. The catalytic efficiencies of the three lipases were in the order of Novozyme 435 > Lipozyme TLIM > Lipozyme RMIM. Furthermore, their catalytic efficiencies in n-hexane were better than those in solvent free media.

Mitochondrial gene rearrangements confirm the parallel evolution of the crab-like form.

PubMed Central

Morrison, C L; Harvey, A W; Lavery, S; Tieu, K; Huang, Y; Cunningham, C W

2002-01-01

The repeated appearance of strikingly similar crab-like forms in independent decapod crustacean lineages represents a remarkable case of parallel evolution. Uncertainty surrounding the phylogenetic relationships among crab-like lineages has hampered evolutionary studies. As is often the case, aligned DNA sequences by themselves were unable to fully resolve these relationships. Four nested mitochondrial gene rearrangements--including one of the few reported movements of an arthropod protein-coding gene--are congruent with the DNA phylogeny and help to resolve a crucial node. A phylogenetic analysis of DNA sequences, and gene rearrangements, supported five independent origins of the crab-like form, and suggests that the evolution of the crab-like form may be irreversible. This result supports the utility of mitochondrial gene rearrangements in phylogenetic reconstruction. PMID:11886621

Catalytic intermolecular carbon electrophile induced semipinacol rearrangement.

PubMed

Zhang, Qing-Wei; Zhang, Xiao-Bo; Li, Bao-Sheng; Xiang, Kai; Zhang, Fu-Min; Wang, Shao-Hua; Tu, Yong-Qiang

2013-02-25

A catalytic intermolecular carbon electrophile induced semipinacol rearrangement was realized and the asymmetric version was also preliminarily accomplished with 92% and 82% ee. The complex tricyclic system architecture with four continuous stereogenic centers could be achieved from simple starting materials in a single step under mild conditions.

RNA-Mediated Epigenetic Programming of Genome Rearrangements

PubMed Central

Nowacki, Mariusz; Shetty, Keerthi; Landweber, Laura F.

2012-01-01

RNA, normally thought of as a conduit in gene expression, has a novel mode of action in ciliated protozoa. Maternal RNA templates provide both an organizing guide for DNA rearrangements and a template that can transport somatic mutations to the next generation. This opportunity for RNA-mediated genome rearrangement and DNA repair is profound in the ciliate Oxytricha, which deletes 95% of its germline genome during development in a process that severely fragments its chromosomes and then sorts and reorders the hundreds of thousands of pieces remaining. Oxytricha’s somatic nuclear genome is therefore an epigenome formed through RNA templates and signals arising from the previous generation. Furthermore, this mechanism of RNA-mediated epigenetic inheritance can function across multiple generations, and the discovery of maternal template RNA molecules has revealed new biological roles for RNA and has hinted at the power of RNA molecules to sculpt genomic information in cells. PMID:21801022

The analysis of ALK gene rearrangement by fluorescence in situ hybridization in non-small cell lung cancer patients

PubMed Central

Krawczyk, Paweł Adam; Ramlau, Rodryg Adam; Szumiło, Justyna; Kozielski, Jerzy; Kalinka-Warzocha, Ewa; Bryl, Maciej; Knopik-Dąbrowicz, Alina; Spychalski, Łukasz; Szczęsna, Aleksandra; Rydzik, Ewelina; Milanowski, Janusz

2013-01-01

Introduction ALK gene rearrangement is observed in a small subset (3–7%) of non-small cell lung cancer (NSCLC) patients. The efficacy of crizotinib was shown in lung cancer patients harbouring ALK rearrangement. Nowadays, the analysis of ALK gene rearrangement is added to molecular examination of predictive factors. Aim of the study The frequency of ALK gene rearrangement as well as the type of its irregularity was analysed by fluorescence in situ hybridisation (FISH) in tissue samples from NSCLC patients. Material and methods The ALK gene rearrangement was analysed in 71 samples including 53 histological and 18 cytological samples. The analysis could be performed in 56 cases (78.87%), significantly more frequently in histological than in cytological materials. The encountered problem with ALK rearrangement diagnosis resulted from the scarcity of tumour cells in cytological samples, high background fluorescence noises and fragmentation of cell nuclei. Results The normal ALK copy number without gene rearrangement was observed in 26 (36.62%) patients ALK gene polysomy without gene rearrangement was observed in 25 (35.21%) samples while in 3 (4.23%) samples ALK gene amplification was found. ALK gene rearrangement was observed in 2 (2.82%) samples from males, while in the first case the rearrangement coexisted with ALK amplification. In the second case, signet-ring tumour cells were found during histopathological examination and this patient was successfully treated with crizotinib with partial remission lasting 16 months. Conclusions FISH is a useful technique for ALK gene rearrangement analysis which allows us to specify the type of gene irregularities. ALK gene examination could be performed in histological as well as cytological (cellblocks) samples, but obtaining a reliable result in cytological samples depends on the cellularity of examined materials. PMID:24592134

QM/MM nonadiabatic dynamics simulations on photoinduced Wolff rearrangements of 1,2,3-thiadiazole

NASA Astrophysics Data System (ADS)

Liu, Xiang-Yang; Fang, Ye-Guang; Xie, Bin-Bin; Fang, Wei-Hai; Cui, Ganglong

2017-06-01

The photoinduced rearrangement reaction mechanism of 1,2,3-thiadiazole remains experimentally elusive. Two possible mechanisms have been proposed to date. The first is a stepwise mechanism via a thiocarbene intermediate; the second is an excited-state concerted rearrangement mechanism. Herein we have adopted both the electronic structure calculations and nonadiabatic dynamics simulations to study the photoinduced rearrangement reactions of 1,2,3-thiadiazole in the S2, S1, and S0 states in solution. On the basis of QM(CASPT2)/MM [quantum mechanics(complete active space self-consistent field second-order perturbation theory)/molecular mechanics] calculations, we have found that (1) the thiocarbene intermediate is not stable; thus, the stepwise mechanism should be unfavorable; (2) the excited-state decay from the S2 via S1 to S0 state is ultrafast and completed within ca. 200 fs; therefore, both the S2 and S1 states should not have a long enough time for the excited-state rearrangements. Instead, we have computationally proposed a modified photoinduced rearrangement mechanism. Upon irradiation, the S2 state is first populated (114.0 kcal/mol), followed by an ultrafast S2 → S1 → S0 excited-state decay along the S-N bond fission, which eventually leads to a very "hot" intermediate with the S-N bond broken (18.3 kcal/mol). Then, thermal rearrangements to thioketene, thiirene, and ethynethiol occur in a concerted asynchronous way. This mechanistic scenario has been verified by full-dimensional trajectory-based nonadiabatic dynamics simulations at the QM(CASPT2)/MM level. Finally, our present computational work provides experimentally interesting mechanistic insights into the photoinduced rearrangement reactions of cyclic and acyclic diazo compounds.

Novel syn intramolecular pathway in base-catalyzed 1,2-elimination reactions of beta-acetoxy esters.

PubMed

Mohrig, Jerry R; Carlson, Hans K; Coughlin, Jane M; Hofmeister, Gretchen E; McMartin, Lea A; Rowley, Elizabeth G; Trimmer, Elizabeth E; Wild, Andrew J; Schultz, Steve C

2007-02-02

As part of a comprehensive investigation of electronic effects on the stereochemistry of base-catalyzed 1,2-elimination reactions, we observed a new syn intramolecular pathway in the elimination of acetic acid from beta-acetoxy esters and thioesters. 1H and 2H NMR investigation of reactions using stereospecifically labeled tert-butyl (2R*,3R*)-3-acetoxy-2,3-2H2-butanoate (1) and its (2R*,3S*) diastereomer (2) shows that 23 +/- 2% syn elimination occurs. The elimination reactions were catalyzed with KOH or (CH3)4NOH in ethanol/water under rigorously non-ion-pairing conditions. By contrast, the more sterically hindered beta-trimethylacetoxy ester produces only 6 +/- 1% syn elimination. These data strongly support an intramolecular (Ei) syn path for elimination of acetic acid, most likely through the oxyanion produced by nucleophilic attack at the carbonyl carbon of the beta-acetoxy group. The analogous thioesters, S-tert-butyl (2R*,3R*)-3-acetoxy-2,3-2H2-butanethioate (3) and its (2R*,3S*) diastereomer (4), showed 18 +/- 2% syn elimination, whereas the beta-trimethylacetoxy substrate gave 5 +/- 1% syn elimination. The more acidic thioester substrates do not produce an increased amount of syn stereoselectivity even though their elimination reactions are at the E1cb interface.

Dipeptide derivative synthesis catalyzed by Pseudomonas aeruginosa elastase.

PubMed

Rival, S; Besson, C; Saulnier, J; Wallach, J

1999-02-01

Pseudomonas aeruginosa elastase was used to synthesize various N-protected dipeptide amides. The identity of the products was confirmed by FAB(+)-MS. After recrystallization, the yield of their synthesis was calculated, their purity was checked by RP-HPLC and their melting point was measured. With regard to the hydrolysis, it is well-established that the enzyme prefers hydrophobic amino acids in P'1 position and it has a wide specificity for the P1 position. This specificity was demonstrated to be quite unchanged when comparing the initial rates of peptide bond formation between different carboxyl donors (Z-aa) and nucleophiles (aa-NH2). The elastase, but not the thermolysin, was notably able to incorporate tyrosine and tryptophan in P'1 position. Furthermore, synthesis initial rates were at least 100 times faster with the elastase. To overcome the problematic condensation of some amino acids during chemical peptide synthesis, it has been previously suggested that enzymatic steps can combine with a chemical strategy. We demonstrated that the elastase readily synthesizes dipeptide derivatives containing various usual N-protecting groups. It was especially able to condense phenylalaninamide to Fmoc- and Boc-alanine. Increasing interest in peptides containing unnatural amino acids led us to try the elastase-catalyzed synthesis of Z-dipeptide amides including those amino acids in the P1 position. A synthesis was demonstrated with alphaAbu, Nle, Nva and Phg.

Thermostable Lipoxygenase, a Key Enzyme in the Conversion of Linoleic Acid into Thrihydroxy-octadecenoic Acid by Pseudomonas aeruginosa PR3

USDA-ARS?s Scientific Manuscript database

Lipoxygenases (LOX) constitute a family of lipid-peroxidizing enzymes catalyzing the oxidation of unsaturated fatty acid with (1Z,4Z)-pentadiene structural unit, leading to formation of the conjugated (Z,E)-hydroperoxydienoic acid. LOXs have been known to be widely distributed in plants and animals...

Spatially rearranged object parts can facilitate perception of intact whole objects.

PubMed

Cacciamani, Laura; Ayars, Alisabeth A; Peterson, Mary A

2014-01-01

The familiarity of an object depends on the spatial arrangement of its parts; when the parts are spatially rearranged, they form a novel, unrecognizable configuration. Yet the same collection of parts comprises both the familiar and novel configuration. Is it possible that the collection of familiar parts activates a representation of the intact familiar configuration even when they are spatially rearranged? We presented novel configurations as primes before test displays that assayed effects on figure-ground perception from memories of intact familiar objects. In our test displays, two equal-area regions shared a central border; one region depicted a portion of a familiar object. Previous research with such displays has shown that participants are more likely to perceive the region depicting a familiar object as the figure and the abutting region as its ground when the familiar object is depicted in its upright orientation rather than upside down. The novel primes comprised either the same or a different collection of parts as the familiar object in the test display (part-rearranged and control primes, respectively). We found that participants were more likely to perceive the familiar region as figure in upright vs. inverted displays following part-rearranged primes but not control primes. Thus, priming with a novel configuration comprising the same familiar parts as the upcoming figure-ground display facilitated orientation-dependent effects of object memories on figure assignment. Similar results were obtained when the spatially rearranged collection of parts was suggested on the groundside of the prime's border, suggesting that familiar parts in novel configurations access the representation of their corresponding intact whole object before figure assignment. These data demonstrate that familiar parts access memories of familiar objects even when they are arranged in a novel configuration.

Spatially rearranged object parts can facilitate perception of intact whole objects

PubMed Central

Cacciamani, Laura; Ayars, Alisabeth A.; Peterson, Mary A.

2014-01-01

The familiarity of an object depends on the spatial arrangement of its parts; when the parts are spatially rearranged, they form a novel, unrecognizable configuration. Yet the same collection of parts comprises both the familiar and novel configuration. Is it possible that the collection of familiar parts activates a representation of the intact familiar configuration even when they are spatially rearranged? We presented novel configurations as primes before test displays that assayed effects on figure-ground perception from memories of intact familiar objects. In our test displays, two equal-area regions shared a central border; one region depicted a portion of a familiar object. Previous research with such displays has shown that participants are more likely to perceive the region depicting a familiar object as the figure and the abutting region as its ground when the familiar object is depicted in its upright orientation rather than upside down. The novel primes comprised either the same or a different collection of parts as the familiar object in the test display (part-rearranged and control primes, respectively). We found that participants were more likely to perceive the familiar region as figure in upright vs. inverted displays following part-rearranged primes but not control primes. Thus, priming with a novel configuration comprising the same familiar parts as the upcoming figure-ground display facilitated orientation-dependent effects of object memories on figure assignment. Similar results were obtained when the spatially rearranged collection of parts was suggested on the groundside of the prime's border, suggesting that familiar parts in novel configurations access the representation of their corresponding intact whole object before figure assignment. These data demonstrate that familiar parts access memories of familiar objects even when they are arranged in a novel configuration. PMID:24904495

LCR-initiated rearrangements at the IDS locus, completed with Alu-mediated recombination or non-homologous end joining.

PubMed

Oshima, Junko; Lee, Jennifer A; Breman, Amy M; Fernandes, Priscilla H; Babovic-Vuksanovic, Dusica; Ward, Patricia A; Wolfe, Lynne A; Eng, Christine M; Del Gaudio, Daniela

2011-07-01

Mucopolysaccharidosis type II (MPS II) is caused by mutations in the IDS gene, which encodes the lysosomal enzyme iduronate-2-sulfatase. In ∼20% of MPS II patients the disorder is caused by gross IDS structural rearrangements. We identified two male cases harboring complex rearrangements involving the IDS gene and the nearby pseudogene, IDSP1, which has been annotated as a low-copy repeat (LCR). In both cases the rearrangement included a partial deletion of IDS and an inverted insertion of the neighboring region. In silico analyses revealed the presence of repetitive elements as well as LCRs at the junctions of rearrangements. Our models illustrate two alternative consequences of rearrangements initiated by non-allelic homologous recombination of LCRs: resolution by a second recombination event (that is, Alu-mediated recombination), or resolution by non-homologous end joining repair. These complex rearrangements have the potential to be recurrent and may be present among those MSP II cases with previously uncharacterized aberrations involving IDS.

A General Method for Copper-Catalyzed Arene Cross-Dimerization

PubMed Central

Do, Hien-Quang; Daugulis, Olafs

2011-01-01

A general method for a highly regioselective, copper-catalyzed cross-coupling of two aromatic compounds by using iodine oxidant has been developed. The reactions involve an initial iodination of one arene followed by arylation of the most acidic C-H bond of the other coupling component. Cross-coupling of electron-rich arenes, electron-poor arenes, five- and six-membered heterocycles is possible in many combinations. Typically, 1/1.5 to 1/3 ratio of coupling components is used in contrast to existing methodology that often employs a large excess of one of the arenes. Common functionalities such as ester, ketone, aldehyde, ether, nitrile, nitro, and amine are well-tolerated. PMID:21823581

Kinetics of acid-catalyzed cleavage of procyanindins

Treesearch

Richard W. Hemingway; Gerald W. McGraw

1983-01-01

Comparison of the rates of cleavage of isomeric procyanidin dimers in the presence of excess phenylmethane thiol and acetic acid showed that compounds with a C(4)-C(8) interflavanoid bond were cleaved more rapidly than their C(4)-C(6) linked isomers, that 2,3-cis isomers with an axial flavan substituent were cleaved more-rapidly than a 2,3-...

Genomic characterization of two large Alu-mediated rearrangements of the BRCA1 gene.

PubMed

Peixoto, Ana; Pinheiro, Manuela; Massena, Lígia; Santos, Catarina; Pinto, Pedro; Rocha, Patrícia; Pinto, Carla; Teixeira, Manuel R

2013-02-01

To determine whether a large genomic rearrangement is actually novel and to gain insight about the mutational mechanism responsible for its occurrence, molecular characterization with breakpoint identification is mandatory. We here report the characterization of two large deletions involving the BRCA1 gene. The first rearrangement harbored a 89,664-bp deletion comprising exon 7 of the BRCA1 gene to exon 11 of the NBR1 gene (c.441+1724_oNBR1:c.1073+480del). Two highly homologous Alu elements were found in the genomic sequences flanking the deletion breakpoints. Furthermore, a 20-bp overlapping sequence at the breakpoint junction was observed, suggesting that the most likely mechanism for the occurrence of this rearrangement was nonallelic homologous recombination. The second rearrangement fully characterized at the nucleotide level was a BRCA1 exons 11-15 deletion (c.671-319_4677-578delinsAlu). The case harbored a 23,363-bp deletion with an Alu element inserted at the breakpoints of the deleted region. As the Alu element inserted belongs to a still active AluY family, the observed rearrangement could be due to an insertion-mediated deletion mechanism caused by Alu retrotransposition. To conclude, we describe the breakpoints of two novel large deletions involving the BRCA1 gene and analysis of their genomic context allowed us to gain insight about the respective mutational mechanism.

Enhancement of nitric oxide release and hemocompatibility by surface chirality of D-tartaric acid grafting

NASA Astrophysics Data System (ADS)

Han, Honghong; Wang, Ke; Fan, Yonghong; Pan, Xiaxin; Huang, Nan; Weng, Yajun

2017-12-01

Nitric Oxide (NO) generation from endogenous NO-donors catalyzed by diselenide modified biomaterials has been reported. Here we reported surface chirality by L-tartaric acid and D-tartaric acid grafting on the outermost showed a significant impact on diselenide modified biomaterials, which modulated protein adsorption, NO release and anti-platelet adhesion properties. D-tartaric acid grafted surface showed more blood protein adsorption than that of L-surfaces by QCM analysis, however, ELISA analysis disclosed less fibrinogen denatured on the D surfaces. Due to the surface ratio of selenium decreasing, NO release catalyzed by L-tartaric acid grafting on the outermost significantly decreased in comparison to that of only selenocystamine immobilized surfaces. While NO release catalyzed by D-tartaric acid grafting on the outermost didn't decrease and was similar with that of selenocystamine immobilized surfaces. Surface chirality combined with NO release had synergetic effects on platelet adhesion, and it showed the lowest number of platelets adhered on the D-tartaric acid grafted surfaces. Thus surface chirality from D-tartaric acid grafting enhanced hemocompatibility of the surface in this study. Our work provides new insights into engineering novel blood contacting biomaterials by taking into account surface chirality.

Divergent synthesis and chemical reactivity of bicyclic lactone fragments of complex rearranged spongian diterpenes.

PubMed

Schnermann, Martin J; Beaudry, Christopher M; Genung, Nathan E; Canham, Stephen M; Untiedt, Nicholas L; Karanikolas, Breanne D W; Sütterlin, Christine; Overman, Larry E

2011-11-02

The synthesis and direct comparison of the chemical reactivity of the two highly oxidized bicyclic lactone fragments found in rearranged spongian diterpenes (8-substituted 6-acetoxy-2,7-dioxabicyclo[3.2.1]octan-3-one and 6-substituted 7-acetoxy-2,8-dioxabicyclo[3.3.0]octan-3-one) are reported. Details of the first synthesis of the 6-acetoxy-2,7-dioxabicyclo[3.2.1]octan-3-one ring system, including an examination of several possibilities for the key bridging cyclization reaction, are described. In addition, the first synthesis of 7-acetoxy-2,8-dioxabicyclo[3.3.0]octanones containing quaternary carbon substituents at C6 is disclosed. Aspects of the chemical reactivity and Golgi-modifying properties of these bicyclic lactone analogs of rearranged spongian diterpenes are also reported. Under both acidic and basic conditions, 8-substituted 2,7-dioxabicyclo[3.2.1]octanones are converted to 6-substituted-2,8-dioxabicyclo[3.3.0]octanones. Moreover, these dioxabicyclic lactones react with primary amines and lysine side chains of lysozyme to form substituted pyrroles, a conjugation that could be responsible for the unique biological properties of these compounds. These studies demonstrate that acetoxylation adjacent to the lactone carbonyl group, in either the bridged or fused series, is required to produce fragmented Golgi membranes in the pericentriolar region that is characteristic of macfarlandin E.

Cytochromes P450 Catalyze the Reduction of α,β-Unsaturated Aldehydes

PubMed Central

Amunom, Immaculate; Dieter, Laura J.; Tamasi, Viola; Cai, Jan; Conklin, Daniel J.; Srivastava, Sanjay; Martin, Martha V.; Guengerich, F. Peter; Prough, Russell A.

2011-01-01

The metabolism of α,β-unsaturated aldehydes, e.g. 4-hydroxynonenal, involves oxidation to carboxylic acids, reduction to alcohols, and glutathionylation to eventually form mercapturide conjugates. Recently we demonstrated that P450s can oxidize aldehydes to carboxylic acids, a reaction previously thought to involve aldehyde dehydrogenase. When recombinant cytochrome P450 3A4 was incubated with 4-hydroxynonenal, O2, and NADPH, several products were produced, including 1,4-dihydroxynonene (DHN), 4-hydroxy-2-nonenoic acid (HNA), and an unknown metabolite. Several P450s catalyzed the reduction reaction in the order (human) P450 2B6 ≅ P450 3A4 > P450 1A2 > P450 2J2 > (mouse) P450 2c29. Other P450s did not catalyze the reduction reaction (human P450 2E1 & rabbit P450 2B4). Metabolism by isolated rat hepatocytes showed that HNA formation was inhibited by cyanamide, while DHN formation was not affected. Troleandomycin increased HNA production 1.6-fold while inhibiting DHN formation, suggesting that P450 3A11 is a major enzyme involved in rat hepatic clearance of 4-HNE. A fluorescent assay was developed using 9-anthracenealdehyde to measure both reactions. Feeding mice diet containing t-butylated hydroxyanisole increased the level of both activities with hepatic microsomal fractions, but not proportionally. Miconazole (0.5 mM) was a potent inhibitor of these microsomal reduction reactions, while phenytoin and α-naphthoflavone (both at 0.5 mM) were partial inhibitors, suggesting the role of multiple P450 enzymes. The oxidative metabolism of these aldehydes was inhibited >90% in an Ar or CO atmosphere, while the reductive reactions were not greatly affected. These results suggest that P450s are significant catalysts of reduction of α,β-unsaturated aldehydes in liver. PMID:21766881

Carbon Isotope Systematics in Mineral-Catalyzed Hydrothermal Organic Synthesis Processes at High Temperature and Pressures

NASA Technical Reports Server (NTRS)

Fu, Qi; Socki, R. A.; Niles, Paul B.

2011-01-01

Observation of methane in the Martian atmosphere has been reported by different detection techniques. Reduction of CO2 and/or CO during serpentization by mineral surface catalyzed Fischer-Tropsch Type (FTT) synthesis may be one possible process responsible for methane generation on Mars. With the evidence a recent study has discovered for serpentinization in deeply buried carbon rich sediments, and more showing extensive water-rock interaction in Martian history, it seems likely that abiotic methane generation via serpentinization reactions may have been common on Mars. Experiments involving mineral-catalyzed hydrothermal organic synthesis processes were conducted at 750 C and 5.5 Kbars. Alkanes, alcohols and carboxylic acids were identified as organic compounds. No "isotopic reversal" of delta C-13 values was observed for alkanes or carboxylic acids, suggesting a different reaction pathway than polymerization. Alcohols were proposed as intermediaries formed on mineral surfaces at experimental conditions. Carbon isotope data were used in this study to unravel the reaction pathways of abiotic formation of organic compounds in hydrothermal systems at high temperatures and pressures. They are instrumental in constraining the origin and evolution history of organic compounds on Mars and other planets.

Elevated Rate of Genome Rearrangements in Radiation-Resistant Bacteria.

PubMed

Repar, Jelena; Supek, Fran; Klanjscek, Tin; Warnecke, Tobias; Zahradka, Ksenija; Zahradka, Davor

2017-04-01

A number of bacterial, archaeal, and eukaryotic species are known for their resistance to ionizing radiation. One of the challenges these species face is a potent environmental source of DNA double-strand breaks, potential drivers of genome structure evolution. Efficient and accurate DNA double-strand break repair systems have been demonstrated in several unrelated radiation-resistant species and are putative adaptations to the DNA damaging environment. Such adaptations are expected to compensate for the genome-destabilizing effect of environmental DNA damage and may be expected to result in a more conserved gene order in radiation-resistant species. However, here we show that rates of genome rearrangements, measured as loss of gene order conservation with time, are higher in radiation-resistant species in multiple, phylogenetically independent groups of bacteria. Comparison of indicators of selection for genome organization between radiation-resistant and phylogenetically matched, nonresistant species argues against tolerance to disruption of genome structure as a strategy for radiation resistance. Interestingly, an important mechanism affecting genome rearrangements in prokaryotes, the symmetrical inversions around the origin of DNA replication, shapes genome structure of both radiation-resistant and nonresistant species. In conclusion, the opposing effects of environmental DNA damage and DNA repair result in elevated rates of genome rearrangements in radiation-resistant bacteria. Copyright © 2017 Repar et al.

Highly Efficient Cu(I)-Catalyzed Oxidation of Alcohols to Ketones and Aldehydes with Diaziridinone

PubMed Central

Zhu, Yingguang; Zhao, Baoguo

2013-01-01

A novel and efficient Cu(I)-catalyzed oxidation of alcohols has been achieved with di-tert-butyldiaziridinone as oxidant under mild conditions. A wide variety of primary and secondary alcohols with various functional groups can be oxidized to aldehydes and ketones in high yields. The reaction proceeds under neutral conditions making it compatible with acid or base-sensitive substrates, and it is amenable to gram scale. PMID:23413952

ROS1 rearrangement and response to crizotinib in Stage IV non-small cell lung cancer

PubMed Central

Suryavanshi, Moushumi; Panigrahi, Manoj Kumar; Kumar, Dushyant; Verma, Haristuti; Saifi, Mumtaz; Dabas, Bharti; Batra, Ullas; Doval, Dinesh; Mehta, Anurag

2017-01-01

Background: The frequency of ROS1 rearrangement in non-small cell lung cancers has been reported from 1.6% to 2.3%. Materials and Methods: We examined 105 lung adenocarcinoma patients for ROS1 rearrangement which were negative for EGFR and anaplastic lymphoma kinase. Clinical characteristics of ROS1 rearranged patients and their responses to crizotinib therapy were studied. Results: Of the 105 patients, three cases were positive for ROS1 rearrangement by fluorescence in situ hybridization analysis. All of them showed heterogeneous pattern. All the 3 ROS1-positive patients were females in their forties and started on crizotinib. All of them responded to treatment. One of them developed resistance after 3 months. Another one showed marked systemic response but central nervous system lesions progressed. The third case is doing well till date with inactive lesions on positron emission tomography scan. Conclusions: The frequency of ROS1 rearrangement is low in non-small cell lung carcinoma, but their diagnosis offers patients an opportunity to receive highly effective targeted therapies. PMID:28869223

Lecture Capture with Real-Time Rearrangement of Visual Elements: Impact on Student Performance

ERIC Educational Resources Information Center

Yu, P.-T.; Wang, B.-Y.; Su, M.-H.

2015-01-01

The primary goal of this study is to create and test a lecture-capture system that can rearrange visual elements while recording is still taking place, in such a way that student performance can be positively influenced. The system we have devised is capable of integrating and rearranging multimedia sources, including learning content, the…

Catalyzed and Electrocatalyzed Oxidation of l-Tyrosine and l-Phenylalanine to Dopachrome by Nanozymes.

PubMed

Hou, Jianwen; Vázquez-González, Margarita; Fadeev, Michael; Liu, Xia; Lavi, Ronit; Willner, Itamar

2018-06-13

Catalyzed oxygen insertion into C-H bonds represents a continuous challenge in chemistry. Particularly, driving this process at ambient temperature and aqueous media represents a "holy grail" in catalysis. We report on the catalyzed cascade transformations of l-tyrosine or l-phenylalanine to dopachrome in the presence of l-ascorbic acid/H 2 O 2 as oxidizing mixture and CuFe-Prussian Blue-like nanoparticles, Fe 3 O 4 nanoparticles or Au nanoparticles as catalysts. The process involves the primary transformation of l-tyrosine to l-DOPA that is further oxidized to dopachrome. The transformation of l-phenylalanine to dopachrome in the presence of CuFe-Prussian Blue-like nanoparticles and l-ascorbic acid/H 2 O 2 involves in the first step the formation of l-tyrosine and, subsequently, the operation of the catalytic oxidation cascade of l-tyrosine to l-DOPA and dopachrome. Electron spin resonance experiments demonstrate that ascorbate radicals and hydroxyl radicals play cooperative functions in driving the different oxygen-insertion processes. In addition, the aerobic elecrocatalyzed oxidation of l-tyrosine to dopachrome in the presence of naphthoquinone-modified Fe 3 O 4 nanoparticles and l-ascorbic acid is demonstrated. In this system, magnetic-field attraction of the naphthoquinone-modified Fe 3 O 4 nanoparticles onto the electrode allows the quinone-mediated electrocatalyzed reduction of O 2 to H 2 O 2 (bias potential -0.5 V vs SCE). The electrogenerated H 2 O 2 is then utilized to promote the transformation of l-tyrosine to dopachrome in the presence of l-ascorbic acid and Fe 3 O 4 catalyst.

Intratumor Heterogeneity of ALK-Rearrangements and Homogeneity of EGFR-Mutations in Mixed Lung Adenocarcinoma

PubMed Central

Marino, Federica Zito; Liguori, Giuseppina; Aquino, Gabriella; La Mantia, Elvira; Bosari, Silvano; Ferrero, Stefano; Rosso, Lorenzo; Gaudioso, Gabriella; De Rosa, Nicla; Scrima, Marianna; Martucci, Nicola; La Rocca, Antonello; Normanno, Nicola; Morabito, Alessandro; Rocco, Gaetano; Botti, Gerardo; Franco, Renato

2015-01-01

Background Non Small Cell Lung Cancer is a highly heterogeneous tumor. Histologic intratumor heterogeneity could be ‘major’, characterized by a single tumor showing two different histologic types, and ‘minor’, due to at least 2 different growth patterns in the same tumor. Therefore, a morphological heterogeneity could reflect an intratumor molecular heterogeneity. To date, few data are reported in literature about molecular features of the mixed adenocarcinoma. The aim of our study was to assess EGFR-mutations and ALK-rearrangements in different intratumor subtypes and/or growth patterns in a series of mixed adenocarcinomas and adenosquamous carcinomas. Methods 590 Non Small Cell Lung Carcinomas tumor samples were revised in order to select mixed adenocarcinomas with available tumor components. Finally, only 105 mixed adenocarcinomas and 17 adenosquamous carcinomas were included in the study for further analyses. Two TMAs were built selecting the different intratumor histotypes. ALK-rearrangements were detected through FISH and IHC, and EGFR-mutations were detected through IHC and confirmed by RT-PCR. Results 10/122 cases were ALK-rearranged and 7 from those 10 showing an intratumor heterogeneity of the rearrangements. 12/122 cases were EGFR-mutated, uniformly expressing the EGFR-mutated protein in all histologic components. Conclusion Our data suggests that EGFR-mutations is generally homogeneously expressed. On the contrary, ALK-rearrangement showed an intratumor heterogeneity in both mixed adenocarcinomas and adenosquamous carcinomas. The intratumor heterogeneity of ALK-rearrangements could lead to a possible impact on the therapeutic responses and the disease outcomes. PMID:26422230

Design and Synthesis of a Library of Tetracyclic Hydroazulenoisoindoles

PubMed Central

Brummond, Kay M.; Mao, Shuli; Shinde, Sunita N.; Johnston, Paul J.; Day, Billy W.

2009-01-01

Forty-four tetracyclic hydroazulenoisoindoles were synthesized via a tandem cyclopropanation/Cope rearrangement followed by a Diels-Alder sequence from easily available five-membered cyclic cross-conjugated trienones. These trienones were obtained from two different routes depending upon whether R1 and R2 are alkyl or amino acid derived functional groups, via a rhodium(I)-catalyzed cycloisomerization reaction. In order to increase diversity, four maleimides and two 1,2,4-triazoline-3,5-diones were used as dienophiles in the Diels-Alder step. Several Diels-Alder adducts were further reacted under palladium-catalyzed hydrogenation conditions, leading to a diastereoselective reduction of the trisubstituted double bond. This library has demonstrated rapid access to a variety of structurally complex natural product-like compounds via stereochemical diversity and building block diversity approaches. PMID:19366169

MicroRNA-106b~25 cluster is upregulated in relapsed MLL-rearranged pediatric acute myeloid leukemia

PubMed Central

Verboon, Lonneke J.; Obulkasim, Askar; de Rooij, Jasmijn D.E.; Katsman, Jenny E.; Sonneveld, Edwin; Baruchel, André; Trka, Jan; Reinhardt, Dirk; Pieters, Rob; Cloos, Jacqueline; Kaspers, Gertjan J.L.; Klusmann, Jan-Henning; Zwaan, Christian Michel; Fornerod, Maarten; van den Heuvel-Eibrink, Marry M.

2016-01-01

The most important reason for therapy failure in pediatric acute myeloid leukemia (AML) is relapse. In order to identify miRNAs that contribute to the clonal evolution towards relapse in pediatric AML, miRNA expression profiling of 127 de novo pediatric AML cases were used. In the diagnostic phase, no miRNA signatures could be identified that were predictive for relapse occurrence, in a large pediatric cohort, nor in a nested mixed lineage leukemia (MLL)-rearranged pediatric cohort. AML with MLL- rearrangements are found in 15-20% of all pediatric AML samples, and reveal a relapse rate up to 50% for certain translocation partner subgroups. Therefore, microRNA expression profiling of six paired initial diagnosis-relapse MLL-rearranged pediatric AML samples (test cohort) and additional eight paired initial diagnosis-relapse samples with MLL-rearrangements (validation cohort) was performed. A list of 53 differentially expressed miRNAs was identified of which the miR-106b~25 cluster, located in intron 13 of MCM7, was the most prominent. These differentially expressed miRNAs however could not predict a relapse in de novo AML samples with MLL-rearrangements at diagnosis. Furthermore, higher mRNA expression of both MCM7 and its upstream regulator E2F1 was found in relapse samples with MLL-rearrangements. In conclusion, we identified the miR-106b~25 cluster to be upregulated in relapse pediatric AML with MLL-rearrangements. PMID:27351222

Comparative linkage mapping of genes on sheep chromosome 3 provides evidence of chromosomal rearrangements in the evolution of the Bovidae.

PubMed

Jenkins, Z A; Henry, H M; Galloway, S M; Dodds, K G; Montgomery, G W

1997-01-01

Three genes--parathyroid hormone-like hormone (PTHLH), insulin-like growth factor 1 (IGF 1), and retinoic acid receptor gamma (RARG)--have been mapped to sheep (Ovis aries) chromosome 3 (OAR 3). The order and genetic distances between loci on OAR 3 are similar to those on cattle (Bos taurus) chromosome 5, as expected from their close evolutionary relationship. The OAR 3 linkage map shows conserved synteny with human chromosome 12, but there are at least two rearrangements in gene order between the species.

Biodiesel production from used cooking oil by two-step heterogeneous catalyzed process.

PubMed

Srilatha, K; Prabhavathi Devi, B L A; Lingaiah, N; Prasad, R B N; Sai Prasad, P S

2012-09-01

The present study demonstrates the production of biodiesel from used cooking oil containing high free fatty acid by a two-step heterogeneously catalyzed process. The free fatty acids were first esterified with methanol using a 25 wt.% TPA/Nb(2)O(5) catalyst followed by transesterification of the oil with methanol over ZnO/Na-Y zeolite catalyst. The catalysts were characterized by XRD, FT-IR, BET surface area and CO(2)-TPD. In the case of transesterification the effect of reaction parameters, such as catalyst concentration, methanol to oil molar ratio and reaction temperature, on the yield of ester were investigated. The catalyst with 20 wt.% ZnO loading on Na-Y exhibited the highest activity among the others. Both the solid acid and base catalysts were found to be reusable for several times indicating their efficacy in the two-step process. Copyright © 2012 Elsevier Ltd. All rights reserved.

Synthesis of oxindole from acetanilide via Ir(iii)-catalyzed C-H carbenoid functionalization.

PubMed

Patel, Pitambar; Borah, Gongutri

2016-12-22

Herein we disclose the first report on the synthesis of oxindole derivatives from acetanilide via Ir(iii)-catalyzed intermolecular C-H functionalization with diazotized Meldrum's acid. A broad range of substituted anilides were found to react smoothly under the Ir(iii)-catalytic system to afford the corresponding N-protected oxindoles. The N-protecting groups, such as Ac, Bz or Piv, can be easily removed to furnish the oxindole. Various synthetic applications of the synthesized oxindole were also demonstrated.