Positronium formation at low temperatures: the role of trapped electrons

Measurements have been carried out of electron spin densities (by electron spin resonance technique) and positronium (Ps) formation probability as functions of Co-60 γ-irradiation dose in poly(methyl methacrylate) and linear poly(ethylene) at 77 K. We observe a linear relationship between the enhancement of the Ps formation and the density of trapped electrons in both polymers. This clear correlation strongly supports the previous suggestion by the authors that the increase in Ps formation with time (that has been observed at low temperatures for a number of polymers) can be explained as a reaction of free positrons with trapped electrons produced by the previously injected positrons.     

A novel four-component reaction for the synthesis of functionalised dihydropyrimidines

In a multi-component reaction (MCR) of a phosphonate, nitriles, aldehydes and isocyanates, N3-functionalised dihydropyrimidines can be synthesised efficiently via a Horner-Emmons/aza Diels-Alder pathway.     

Measurement of Very Fast Exchange Rates of Individual Amide Protons in Proteins by NMR Spectroscopy

NMR spectroscopy is a pivotal technique to measure hydrogen exchange rates in proteins. However, currently available NMR methods to measure backbone exchange are limited to rates of up to a few per second. To raise this limit, we have developed an approach that is capable of measuring proton exchange rates up to approximately 10⁴ s⁻¹. Our method relies on the detection of signal loss due to the decorrelation of antiphase operators 2N_xH_z by exchange events that occur during a series of pi pulses on the ¹⁵N channel. In practice, signal attenuation was monitored in a series of 2D H(CACO)N spectra, recorded with varying pi-pulse spacing, and the exchange rate was obtained by numerical fitting to the evolution of the density matrix. The method was applied to the small calcium-binding protein Calbindin D_9k, where exchange rates up to 600 s⁻¹ were measured for amides, where no signal was detectable in ¹⁵N−¹H HSQC spectra. A temperature variation study allowed us to determine apparent activation energies in the range 47–69 kJ mol⁻¹ for these fast exchanging amide protons, consistent with hydroxide-catalyzed exchange.     

The analysis of C4–C11 hydrocarbons in naphtha and reformate with a new apolar fused silica column

This paper deals with the separation of alkanes, naphthenes, and aromatic compounds in naphtha and reformate, on a newly developed apolar high resolution GC column. The selectivity of this apolar phase has been compared with those of squalane, DB-1, and SE-30. A total of 95 hydrocarbons were reliably identified, mostly by GC-MS. Repeated measurements of Kováts retention indices are presented as evidence for the reproducible manufacture of fused silica columns coated with this phase.     

A self-consistent field study of a hydrocarbon droplet at the air-water interface

A molecularly detailed self-consistent field (SCF) approach is applied to describe a sessile hydrocarbon droplet placed at the air-water interface. Predictions of the contact angle for macroscopic droplets follow from using Neumann's equation, wherein the macroscopic interfacial tensions are computed from one-gradient calculations for flat interfaces. A two-gradient cylindrical coordinate system with mirror-like boundary conditions is used to analyse the three dimensional shape of the nano-scale oil droplet at the air-water interface. These small droplets have a finite value of the Laplace pressure and concomitant line tension. It has been calculated that the oil-water and oil-vapour interfacial tensions are curvature dependent and increase slightly with increasing interfacial curvature. In contrast, the line tension tends to decrease with curvature. In all cases there is only a weak influence of the line tension on the droplet shape. We therefore argue that the nano-scale droplets, which are described in the SCF approach, are representative for macroscopic droplets and that the method can be used to efficiently generate accurate information on the spreading of oil droplets at the air-water interface in molecularly more complex situations. As an example, non-ionic surfactants have been included in the system to illustrate how a molecularly more complex situation will change the wetting properties of the sessile drop. This short forecast is aimed to outline and to stress the potential of the method.     

A new approach to untargeted integration of high resolution liquid chromatography–mass spectrometry data

Because of its high sensitivity and specificity, hyphenated mass spectrometry has become the predominant method to detect and quantify metabolites present in bio-samples relevant for all sorts of life science studies being executed. In contrast to targeted methods that are dedicated to specific features, global profiling acquisition methods allow new unspecific metabolites to be analyzed. The challenge with these so-called untargeted methods is the proper and automated extraction and integration of features that could be of relevance. We propose a new algorithm that enables untargeted integration of samples that are measured with high resolution liquid chromatography–mass spectrometry (LC–MS). In contrast to other approaches limited user interaction is needed allowing also less experienced users to integrate their data. The large amount of single features that are found within a sample is combined to a smaller list of, compound-related, grouped feature-sets representative for that sample. These feature-sets allow for easier interpretation and identification and as important, easier matching over samples. We show that the automatic obtained integration results for a set of known target metabolites match those generated with vendor software but that at least 10 times more feature-sets are extracted as well. We demonstrate our approach using high resolution LC–MS data acquired for 128 samples on a lipidomics platform. The data was also processed in a targeted manner (with a combination of automatic and manual integration) using vendor software for a set of 174 targets. As our untargeted extraction procedure is run per sample and per mass trace the implementation of it is scalable. Because of the generic approach, we envision that this data extraction lipids method will be used in a targeted as well as untargeted analysis of many different kinds of TOF-MS data, even CE- and GC–MS data or MRM. The Matlab package is available for download on request and efforts are directed toward a user-friendly Windows executable.     

Slow internal dynamics in proteins: application of NMR relaxation dispersion spectroscopy to methyl groups in a cavity mutant of T4 lysozyme

Recently developed carbon transverse relaxation dispersion experiments (Skrynnikov, N. R.; et al. J. Am. Chem. Soc. 2001, 123, 4556-4566) were applied to the study of millisecond to microsecond time scale motions in a cavity mutant of T4 lysozyme (L99A) using methyl groups as probes of dynamics. Protein expressed in E. coli cells with (13)CH(3)-pyruvate as the sole carbon source contained high levels of (13)C enrichment at a total of 80 Val gamma, Leu delta, Ile gamma (2), Ala beta, and Met epsilon methyl positions with little extraneous incorporation. Data for 72 methyl groups were available for analysis. Dispersion profiles with large amplitudes were measured for many of these residues and were well fit to a two-state exchange model. The interconversion rates and populations of the states, obtained from fitting relaxation dispersion profiles of each individual probe, were remarkably homogeneous and data for nearly all methyl groups in the protein could be collectively fit to a single cooperative conformational transition. The present study demonstrates the general applicability of methyl relaxation dispersion measurements for the investigation of millisecond time scale protein motions at a large number of side-chain positions. Potential artifacts associated with the experiments are described and methods to minimize their effects presented. These experiments should be particularly well suited for probing dynamics in high molecular weight systems due to the favorable NMR spectroscopic properties of methyl groups.     

Methylene-azaphosphirane as a reactive intermediate

Reaction of the transient phosphinidene complexes R-P=W(CO)5 with N-substituted-diphenylketenimines leads unexpectedly to the novel 2-aminophosphindoles, as confirmed by an X-ray crystal structure determined for one of the derivatives. Experimental evidence for a methylene-azaphosphirane intermediate was found by using the iron-complexed phosphinidene iPr2N-P=Fe(CO)4, which affords the 2-aminophosphindole together with the novel methylene-2,3-dihydro-1H-benzo[1,3]azaphosphole. Analysis of the reaction pathways with DFT indicates that the initially formed methylene-azaphosphirane yields both phosphorus heterocycles by way of a [1,5]- or [1,3]-sigmatropic shift, respectively, followed by a H-shift. Strain underlies both rearrangements, which causes these remarkably selective conversions that can be tuned by changing the substituents.     

4-metalated condensed pyrimidines: their preparation and reaction with aldehydes under Barbier-type conditions

[reaction: see text] The organometallic intermediate obtained from halogen-metal exchanges of 4-iodo-6-phenylthieno[2,3-d]pyrimidine under Barbier-type conditions was reacted with aldehydes to form the corresponding alcohols in moderate yields. The reaction involving an organolithium intermediate proceeded only at low temperature, whereas the reaction involving a magnesium ate intermediate also proceeded at room temperature. A crystal structure confirms that the expected constitutional alcohol isomer is formed, where no migration has taken place. The conditions were also suitable for 9-benzyl-6-iodopurine.