Asymmetric homogeneous hydrogenations at scale.

Asymmetric hydrogenations are increasingly being used to introduce stereogenic centres into products used in the life sciences industries. There are a number of potential pitfalls when moving from a laboratory reaction to a manufacturing process, not least of which is safety. Time-to-market pressure leads to short development times, which in the past could be a large barrier for the implementation of catalytic steps; now there are new ways to minimise this problem. The potential problems associated with impurities and other methods that can shut down the hydrogenation reactions are highlighted in this critical review (353 references).

Open window thoracostomy treatment of empyema is accelerated by vacuum-assisted closure.

BACKGROUND: Recurrent thoracic empyema in the presence of residual lung tissue can be treated with an open window thoracostomy (OWT). Vacuum-assisted closure (VAC) of these large thoracic defects is a novel option. METHODS: Nineteen patients with residual lung tissue received an OWT for treatment of recurrent thoracic empyema. In this retrospective case series, 8 patients (aged 58 +/- 20 years, all male) were treated conventionally, and 11 patients (aged 53 +/- 17 years, 8 male) were treated with VAC. RESULTS: The application of the VAC system resulted in rapid debridement of the thoracic cavity and reexpansion of the residual lung tissue. The duration of OWT and VAC therapy was 39 +/- 17 and 31 +/- 19 days, respectively. All 11 patients were amenable for subsequent closure using pedicled muscular flaps. In 2 patients, VAC therapy alone resulted in complete closure of the OWT. The average duration of follow-up was 46 +/- 19 months. All patients, except 1, have recovered well. One patient died of nonpulmonary causes. In the non-VAC group (n = 8), the OWT was managed conventionally by application of saline-soaked gauzes. In 2 patients, the OWT was eventually closed using pedicled muscular flaps (after 75 and 440 days, respectively). Four patients died of OWT-related complications (1 bleeding, 3 recurrent infections) during follow-up; 1 patient died of a cause unrelated to OWT. The average duration of OWT was 933 +/- 1,422 days. CONCLUSIONS: When compared with conventional management of OWT, VAC therapy accelerates wound healing and improves reexpansion of residual lung tissue in patients with OWT after empyema, allowing rapid surgical closure.

The two-component colR/S system of Pseudomonas fluorescens WCS365 plays a role in rhizosphere competence through maintaining the structure and function of the outer membrane.

Pseudomonas fluorescens strain PCL1210, a competitive tomato root tip colonization mutant of the efficient root colonizing wild type strain WCS365, is impaired in the two-component sensor-response regulator system ColR/ColS. Here we show that a putative methyltransferase/wapQ operon is located downstream of colR/colS and that this operon is regulated by ColR/ColS. Since wapQ encodes a putative lipopolysaccharide (LPS) phosphatase, the possibility was studied that the integrity of the outer membrane of PCL1210 was altered. Indeed, it was shown that mutant PCL1210 is more resistant to various chemically unrelated antibiotics which have to pass the outer membrane for their action. In contrast, the mutant is more sensitive to the LPS-binding antibiotic polymyxin B. Mutant PCL1210 loses growth in competition with its wild type when grown in tomato root exudate. Mutants in the methyltransferase/wapQ operon are also altered in their outer membrane permeability and are defective in competitive tomato root tip colonization. A model for the altered outer membrane of PCL1210 is discussed.

Exploiting noninnocent (E,E)-dibenzylideneacetone (dba) effects in palladium(0)-mediated cross-coupling reactions: modulation of the electronic properties of dba affects catalyst activity and stability in ligand and ligand-free reaction systems.

The reactivity of palladium(0) complexes, [Pd(0) (2)(dba-n,n'-Z)(3)] (n,n'-Z=4,4'-F; 4,4'-CF(3); 4,4'-H; 4,4'-MeO) and [Pd(0)(dba-n,n'-Z)(2)] (n,n'-Z=4,4'-CF(3); 4,4'-H; 3,3',5,5'-OMe), used as precursor catalysts with suitable donor ligands (e.g. phosphines, N-heterocyclic carbenes), has been correlated in several palladium(0)-mediated cross-coupling processes. Increasing the electron density on the aryl moiety of the dba-n,n'-Z ligand increases the overall catalytic activity in the majority of these processes. This effect primarily derives from destabilization of the L(n)Pd(0)-eta(2)-dba interaction (in dpi-pi* synergic bonding, n=1 or 2), which ultimately increases the global concentration of catalytically active L(n)Pd(0) available for reaction with aryl halide in the first committed step in the general catalytic cycle(s) (oxidative addition). Decreasing electron density on the aryl moiety of the dba-n,n'-Z ligand stabilizes the Pd(0)-eta(2)-dba interaction, reducing catalytic activity. The specific type of dba-n,n'-Z ligand appears to also play a stabilizing role in the catalytic cycle, preventing Pd agglomeration, and increasing catalyst longevity. A subtle balance therefore exists between the L(n)Pd(0) concentration (and the associated catalytic activity) and catalyst longevity. Changing the type of dba-n,n'-Z ligand controls the concentration of L(n)Pd(0) and the rate of the oxidative addition step, and not other intimate steps within the catalytic cycle(s), for example, transmetallation (or carbopalladation) and reductive elimination. The role of dba-n,n'-Z ligands in Heck arylation is more convoluted and dependent on the alkene substrate employed, although trends have emerged. Changes in the structure of dba-n,n'-Z had a minimal affect on Buchwald-Hartwig aryl amination processes. A secondary Michael reaction of dba-n,n'-Z with amine and/or base effectively lessens its interference in the catalytic cycle.

Rh-catalyzed asymmetric hydrogenation of prochiral olefins with a dynamic library of chiral TROPOS phosphorus ligands.

A library of 19 chiral tropos phosphorus ligands, based on a flexible (tropos) biphenol unit and a chiral P-bound alcohol (11 phosphites) or secondary amine (8 phosphoramidites), was synthesized. These ligands were screened, individually and as a combination of two, in the rhodium-catalyzed asymmetric hydrogenation of dehydro-alpha-amino acids, dehydro-beta-amino acids, enamides and dimethyl itaconate. ee values up to 98% were obtained for the dehydro-alpha-amino acids, by using the best combination of ligands, a phosphite [4-P(O)2O] and a phosphoramidite [13-P(O)2N]. Kinetic studies of the reactions with the single ligands and with the combination of phosphite [4-P(O)2O] and phosphoramidite [13-P(O)2N] have shown that the phosphite, despite being less enantioselective, promotes the hydrogenation of methyl 2-acetamidoacrylate and methyl 2-acetamidocinnamate faster than the mixture of the same phosphite with the phosphoramidite, while the phosphoramidite alone is much less active. In this way, the reaction was optimized by lowering the phosphite/phosphoramidite ratio (the best ratio is 0.25 equiv phosphite/1.75 equiv phosphoramidite) with a resulting improvement of the product enantiomeric excess. A simple mathematical model for a better understanding of the variation of the enantiomeric excess with the phosphite/phosphoramidite ratio is also presented.

Cycloruthenated primary and secondary amines as efficient catalyst precursors for asymmetric transfer hydrogenation.

[reaction: see text] Ruthenacycles obtained by cyclometalation of enantiopure aromatic primary or secondary amines with [(eta6-benzene)RuCl2]2 or with [(eta6-p-cymene)RuCl2]2 are efficient catalysts for asymmetric transfer hydrogenation (TOF up to 190 h(-1) at room temperature). Enantioselectivities in the transfer hydrogenation of acetophenone ranged from 38% to 89%. It is possible to prepare the catalysts in situ, which allows the use of high throughput experimentation.

Benchmarking the CATMA microarray. A novel tool for Arabidopsis transcriptome analysis.

Transcript profiling is crucial to study biological systems, and various platforms have been implemented to survey mRNAs at the genome scale. We have assessed the performance of the CATMA microarray designed for Arabidopsis (Arabidopsis thaliana) transcriptome analysis and compared it with the Agilent and Affymetrix commercial platforms. The CATMA array consists of gene-specific sequence tags of 150 to 500 bp, the Agilent (Arabidopsis 2) array of 60mer oligonucleotides, and the Affymetrix gene chip (ATH1) of 25mer oligonucleotide sets. We have matched each probe repertoire with the Arabidopsis genome annotation (The Institute for Genomic Research release 5.0) and determined the correspondence between them. Array performance was analyzed by hybridization with labeled targets derived from eight RNA samples made of shoot total RNA spiked with a calibrated series of 14 control transcripts. CATMA arrays showed the largest dynamic range extending over three to four logs. Agilent and Affymetrix arrays displayed a narrower range, presumably because signal saturation occurred for transcripts at concentrations beyond 1,000 copies per cell. Sensitivity was comparable for all three platforms. For Affymetrix GeneChip data, the RMA software package outperformed Microarray Suite 5.0 for all investigated criteria, confirming that the information provided by the mismatch oligonucleotides has no added value. In addition, taking advantage of replicates in our dataset, we conducted a robust statistical analysis of the platform propensity to yield false positive and false negative differentially expressed genes, and all gave satisfactory results. The results establish the CATMA array as a mature alternative to the Affymetrix and Agilent platforms.

Highly enantioselective conjugate additions of potassium organotrifluoroborates to enones by use of monodentate phosphoramidite ligands.

The use of phosphoramidite ligands in the rhodium-catalyzed asymmetric conjugate addition of potassium organotrifluoroborates to various enones in the absence of water is described. A systematic search for effective catalysts has been performed by use of high-throughput screening methods. Initially, we have screened reaction conditions, catalyst precursors, and focused ligand libraries. In the next stage we have used the monodentate ligand combination approach, and finally we have made a library of 96 different phosphoramidites by parallel synthesis in the robot (instant ligand libraries) and have tested these in the vinylation of cyclohexenone (up to 88% enantiomeric excess, ee) and 4-phenyl-3-buten-2-one (up to 42% ee). Arylation of cyclohexenone by use of potassium phenyltrifluoroborate gave 3-phenylcyclohexanone with 99% ee.

Synthesis and application in asymmetric C-C bond formation of solution phase ligand libraries of monodentate phosphoramidites.

A library of 96 unique monodentate phosphoramidite ligands has been synthesized in solution and used in the asymmetric conjugate addition of potassium vinyltrifluoroborate to enones resulting in up to 88% ee.

Instant ligand libraries. Parallel synthesis of monodentate phosphoramidites and in situ screening in asymmetric hydrogenation.

Chiral phosphoramidites have been identified as excellent ligands for various metal-catalyzed enantioselective transformations. Taking advantage of their easy preparation and modular nature, we designed a fully automated protocol for the parallel preparation of a library of 32 phosphoramidites and its screening in asymmetric hydrogenation of amino acid precursors. This initial study led to the discovery of a new ligand for the preparation of an enantiopure beta(3)-homoalanine precursor. [structure--see text]

Interactions in the tomato rhizosphere of two Pseudomonas biocontrol strains with the phytopathogenic fungus Fusarium oxysporum f. sp. radicis-lycopersici.

The fungus Fusarium oxysporum f. sp. radicis-lycopersici causes foot and root rot of tomato plants, which can be controlled by the bacteria Pseudomonas fluorescens WCS365 and P. chlororaphis PCL1391. Induced systemic resistance is thought to be involved in biocontrol by P. fluorescens WCS365. The antifungal metabolite phenazine-1-carboxamide (PCN), as well as efficient root colonization, are essential in the mechanism of biocontrol by P. chlororaphis PCL1391. To understand the effects of bacterial strains WCS365 and PCL1391 on the fungus in the tomato rhizosphere, microscopic analyses were performed using different autofluorescent proteins as markers. Tomato seedlings were inoculated with biocontrol bacteria and planted in an F. oxysporum f. sp. radicis-lycopersici-infested gnotobiotic sand system. Confocal laser scanning microscope analyses of the interactions in the tomato rhizosphere revealed that i) the microbes effectively compete for the same niche, and presumably also for root exudate nutrients; ii) the presence of either of the two bacteria negatively affects infection of the tomato root by the fungus; iii) both biocontrol bacteria colonize the hyphae extensively, which may represent a new mechanism in biocontrol by these pseudomonads; and iv) the production of PCN by P. chlororaphis PCL1391 negatively affects hyphal growth and branching, which presumably affects the colonization and infecting ability of the fungus.

Homeopathic ligand-free palladium as a catalyst in the heck reaction. A comparison with a palladacycle.

[reaction: see text] Ligand-free Pd(OAc)(2) can be used as a catalyst in the Heck reaction of aryl bromides as long as the amount of catalyst is kept between 0.01 and 0.1 mol %. At higher concentrations palladium black forms and the reaction stops. The actual catalyst is monomeric. Palladacycles merely serve as a source of ligand-free palladium in Heck reactions of aryl bromides.

Mono- versus bidentate ligands in rhodium-catalyzed asymmetric hydrogenation. A comparative rate study.

[reaction: see text] Bidentate chiral phosphines are no longer essential for achieving a fast and highly enantioselective hydrogenation of alpha- or beta-dehydroamino acid derivatives. In particular, a readily accessible and stable monodentate phosphoramidite can be highly effective in these asymmetric hydrogenations.

Characterization of NADH dehydrogenases of Pseudomonas fluorescens WCS365 and their role in competitive root colonization.

The excellent-root-colonizing Pseudomonas fluorescens WCS365 was selected previously as the parental strain for the isolation of mutants impaired in root colonization. Transposon mutagenesis of WCS365 and testing for root colonization resulted in the isolation of mutant strain PCL1201, which is approximately 100-fold impaired in competitive tomato root colonization. In this manuscript, we provide evidence that shows that the lack of NADH dehydrogenase I, an enzyme of the aerobic respiratory chain encoded by the nuo operon, is responsible for the impaired root-colonization ability of PCL1201. The complete sequence of the nuo operon (ranging from nuoA to nuoN) of P. fluorescens WCS365 was identified, including the promoter region and a transcriptional terminator consensus sequence downstream of nuoN. It was shown biochemically that PCL1201 is lacking NADH dehydrogenase I activity. In addition, the presence and activity of a second NADH dehydrogenase, encoded by the ndh gene, was identified to our knowledge for the first time in the genus Pseudomonas. Since it was assumed that low-oxygen conditions were present in the rhizosphere, we analyzed the activity of the nuo and the ndh promoters at different oxygen tensions. The results showed that both promoters are up-regulated by low concentrations of oxygen and that their levels of expression vary during growth. By using lacZ as a marker, it was shown that both the nuo operon and the ndh gene are expressed in the tomato rhizosphere. In contrast to the nuo mutant PCL1201, an ndh mutant of WCS365 appeared not to be impaired in competitive root tip colonization.

Selective Pd-catalyzed oxidative coupling of anilides with olefins through C-H bond activation at room temperature.

Using a high-throughput experimentation approach we found a selective and mild Pd-catalyzed oxidative coupling reaction between anilide derivatives and acrylates that occurs through ortho C-H bond activation. The reaction is carried out in an acidic environment and occurs even at room temperature with use of a cheap oxidant (benzoquinone) in yields up to 91%. The benzoquinone possibly also functions as a ligand, stabilizing the catalyst. From the electronic dependence of the reaction and the observed kinetic isotope effect (kH/kD = 3) the key step of the catalytic cycle is believed to be electrophilic attack by a [PdOAc]+ complex on the pi-system of the arene.