What to Learn from a Comparative Genomic Sequence Analysis of L-Carnitine Dehydrogenase

In contrast to eukaryotic cells certain eubacterial strains have acquired the ability to utilize L-carnitine (R-(–)-3-hydroxy-4-(trimethylamino)butyrate) as sole source of energy, carbon and nitrogen. The first step of the L-carnitine degradation to glycine betaine is catalysed by L-carnitine dehydrogenase (L-CDH, EC 1.1.1.108) and results in the formation of the dehydrocarnitine. During the oxidation of L-carnitine a simultaneous conversion of the cofactor NAD⁺ to NADH takes place. This catabolic reaction has always been of keen interest, because it can be exploited for spectroscopic L-carnitine determination in biological fluids – a quantification method, which is developed in our lab – as well as L-carnitine production.Based on a cloned L-CDH sequence an expedition through the currently available prokaryotic genomic sequence space began to mine relevant information about bacterial L-carnitine metabolism hidden in the enormous amount of data stored in public sequence databases. Thus by means of homology-based and context-based protein function prediction is revealed that L-CDH exists in certain eubacterial genomes either as a protein of approximately 35 kDa or as a homologous fusion protein of approximately 54 kDa with an additional putative domain, which is predicted to possess a thioesterase activity. These two variants of the enzyme are found on one hand in the genome sequence of bacterial species, which were previously reported to decompose L-carnitine, and on the other hand in gram-positive bacteria, which were not known to express L-CDH. Furthermore we could not only discover that L-CDH is located in a conserved genetic entity, which genes are very likely involved in this L-carnitine catabolic pathway, but also pinpoint the exact genomic sequence position of several other enzymes, which play an essential role in the bacterial metabolism of L-carnitine precursors.     

LC-MS analysis in the aquatic environment and in water treatment – a critical review

LC-MS has become an invaluable technique for trace analysis of polar compounds in aqueous samples of the environment and in water treatment. LC-MS is of particular importance due to the impetus it has provided for research into the occurrence and fate of polar contaminants, and of their even more polar transformation products. Mass spectrometric detection and identification is most widely used in combination with sample preconcentration, chromatographic separation and atmospheric pressure ionization (API). The focus of the first part of this review is directed particularly toward instruments and method development with respect to their applications for detecting emerging contaminants, microorganisms and humic substances (HS). The current status and future perspectives of 1) mass analyzers, 2) ionization techniques to interface liquid chromatography (LC) with mass spectrometry (MS), 3) methods for preconcentration and separation with respect to their application for water analysis are discussed and examples of applications are given. Quadrupole and ion trap mass analyzers with electrospray ionization (ESI) and atmospheric pressure chemical ionization (APCI) are already applied in routine analysis. Time-of-flight (TOF) mass spectrometers are of particular interest for accurate mass measurements for identification of unknowns. For non-polar compounds, different ionization approaches have been described, such as atmospheric pressure photoionization (APPI), electrochemistry with ESI, or electron capture ionization with APCI. In sample preconcentration and separation, solid phase extraction (SPE) with different non-selective sorbent materials and HPLC on reversed-phase materials (RP-HPLC) play the dominant role. In addition, various on-line and miniaturized approaches for sample extraction and sample introduction into the MS have been used. Ion chromatography (IC), size-exclusion chromatography (SEC), and capillary electrophoresis (CE) are alternative separation techniques. Furthermore, the issues of compound identification, matrix effects on quantitation, development of mass spectral libraries and the topic of connecting analysis and toxicity bioassays are addressed.     

An Evaluation of Ligand Properties of Neutral and Anionic Tris(imidazol‐2‐yl)phosphines

In order to study the applicability of tris(imidazol‐2‐yl)phosphine (PIm₃) as a possible charge‐variable ligand, new neutral N‐butyl and N‐benzyl derivatives and d⁰‐metal complexes thereof were prepared and characterized as reference compounds for planned complexes with high valent metals. In addition, an anionic ligand precursor was characterized by X‐Ray analysis and its reactivity towards transition metal halides assayed.     

Theory and experiment in concert: templated synthesis of amide rotaxanes, catenanes, and knots

The synthesis of amide rotaxanes, amide catenanes, and trefoil amide knots is based on template effects mediated by hydrogen bonds. While a large body of experimental data is available, in-depth theoretical studies of these template syntheses are virtually unavailable, although they would provide a more profound insight into the exact details of the hydrogen-bonding patterns involved in the formation of these mechanically interlocked species. In this article we present a density functional study of the conformational properties of tetralactam macrocycles and the threading mechanism that produces the immediate precursor for rotaxane and catenane formation. Predictions of the geometries and relative energies made on the basis of semi-empirical AM1 calculations are compared with these results in order to judge the reliability of the simpler approach. Since these calculations yield good agreement with the structural features, they have been used to extend the calculations in order to understand the mechanism of formation of a trefoil dodecaamide knot that has recently been synthesized. The inherent topological chirality of the knot is reflected in the intermediates generated during its formation; these involve helical loops. These loops parallel the rotaxane and catenane wheels with respect to the arrangement of the functional groups that mediate the template effect and may well serve as wheel analogues through which one of the precursor molecules can be threaded. This threading step finally results in the knotted structure. Good agreement between the results of the calculations presented here and experimental findings is achieved.     

Immobilization of ruthenium(II) salen complexes on poly(4-vinylpyridine) and their application in catalytic aldehyde olefination

Two Ru(II)(salen)(PPh₃)₂ complexes grafted on poly(4-vinylpyridine) have been synthesized and characterized. An elemental analysis shows that both grafted samples contain ca. 0.6 wt % Ru. FTIR spectra confirm the formation of metal-salen complexes attached to the carrier polymer by an interaction between the ruthenium(II) compounds with the pyridine nitrogen atoms of the poly(4-vinylpyridine). Immobilization of both Ru(II) salen complexes on the polymer increases their thermal stability as demonstrated by TG-MS analysis. The grafted materials were applied as catalysts for the olefination of various aldehydes at 60 °C under an inert gas atmosphere, showing comparable yields as their homogeneous congeners and high trans-selectivities. The ruthenium(II) compound with a larger salen ligand shows a better recyclability and selectivity than the derivative with the smaller ligand.     

Methylrhenium oxides

Reactions of the rhenium(VII) precursors Re₂O₇, acetyl perrhenate, trifluoroacetyl perrhenate, chlorotrioxorhenium and trimethylsilyl perrhenate are performed with various common tin free methylating agents. The yields of MTO and the products of partial reduction, bis[dimethyl(μ-oxo)oxo-rhenium(VI)] and (μ-oxo)bis[trimethyloxorhenium(VI)], are quantified by NMR spectroscopy. With aluminium- and copper-containing methylating agents none of the above mentioned compounds are formed, solely perrhenate and rhenium(VI) oxide are detected. The best result is achieved with trifluoroacetyl perrhenate and dimethylzinc, yielding >60% MTO.     

Utilizing ion mobility to identify isobaric post-translational modifications: resolving acrolein and propionyl lysine adducts by TIMS mass spectrometry

Protein post-translational modifications provide critical proteomic details towards elucidating mechanisms of altered protein function due to toxic exposure, altered metabolism, or disease pathogenesis. Lysine propionylation is a recently described modification that occurs due to metabolic alterations in propionyl-CoA metabolism and sirtuin depropionylase activity. Acrolein is a toxic aldehyde generated through exogenous and endogenous pathways, such as industrial exposure, cigarette smoke inhalation, and non-enzymatic lipid peroxidation. Importantly, lysine modifications arising from propionylation and acroleination can be isobaric – indistinguishable by mass spectrometry – and inseparable via reverse-phase chromatography. Here, we present the novel application of trapped ion mobility spectrometry (TIMS) to resolve such competing isobaric lysine modifications. Specifically, the PTM products of a small synthetic peptide were analyzed using a prototype TIMS – time-of-flight mass spectrometer (TIMS-TOF). In that the mobilities of these propionylated and acroleinated peptides differ by only 1%, a high-resolution mobility analysis is required to resolve the two. We were able to achieve more than sufficient resolution in the TIMS analyzer (~170), readily separating these isobars.     

Analysis of flame retardant additives in polymer fractions of waste of electric and electronic equipment (WEEE) by means of HPLC-UV/MS and GPC-HPLC-UV

An HPLC-UV/MS method has been developed to identify and quantify flame retardants in post-consumer plastics from waste of electric and electronic equipment (WEEE). Atmospheric pressure chemical ionisation spectra of 15 brominated and phosphate-based flame retardants were recorded and interpreted. The method was applied to detect flame retardant additives in polymer extracts obtained from pressurised liquid extraction of solid polymers. In addition, a screening method was developed for soluble styrene polymers to isolate a flame retardant fraction through the application of gel permeation chromatography (GPC). This fraction was transferred to an online-coupled HPLC column and detected by UV spectroscopy, which allowed a reliable qualitative and quantitative analysis of brominated flame retardants in the polymer solutions.     

A shield for reducing the thermal signal from heating holders during in situ energy-dispersive X-ray spectroscopy analysis.

This article describes a simple shield that can be placed on typical commercial heating holders to reduce the thermal signal during heating to reasonable levels for in situ energy-dispersive X-ray spectroscopy analysis. The improved temperature capability provided by the shield is demonstrated by initial compositional analysis results obtained across a solid-liquid interface on Al-Si-Cu-Mg alloy powder particles. Considerations in the design of and improvement for the shield are discussed.