Characterization of free radicals in clathrate hydrates of pyrrole, thiophene and isoxazole by muon spin spectroscopy

Gas hydrates have long been of interest to the petrochemical industry but there has been growing interest in potential applications for carbon dioxide sequestration and hydrogen storage. This has prompted many fundamental studies of structure and host-guest interactions, but there has been relatively little investigation of chemical reactions of the guest molecules. In previous work we have shown that it is possible to use muon spin spectroscopy to characterize H-atom-like muonium and muoniated free radicals formed in clathrate hydrates. Muonium forms in clathrate hydrates of cyclopentane and tetrahydrofuran, whereas furan and its dihydro- derivatives form radicals. The current work extends studies to clathrates hydrates of other 5-membered heterocycles: thiophene, pyrrole and isoxazole. All form structure II hydrates. In addition to the clathrates, pure liquid samples of the heterocycles were studied to aid in the assignment of radical signals and for comparison with the enclathrated radicals. Similar to furan, two distinct radicals are formed when muonium reacts with thiophene and pyrrole. However, only one muoniated radical was detected from isoxazole. Muon, proton and nitrogen hyperfine constants were determined and compared with values predicted by DFT calculations to aid the structure assignments. The results show that Mu adds preferentially to the carbon adjacent to the heteroatom in thiophene and pyrrole, and to the carbon adjacent to O in isoxazole. The same radicals are formed in clathrates, but the spectra have broader signals, suggesting slower tumbling. Furthermore, additional signals in the avoided level-crossing spectra indicate anisotropy consistent with restricted motion of the radicals in the clathrate cages

Characterization of Free Radicals in Clathrate Hydrates of Furan, 2,3-Dihydrofuran and 2,5-Dihydrofuran by Muon Spin Spectroscopy

In addition to their importance as abundant hydrocarbon deposits in nature, clathrate hydrates are being studied as potential media for hydrogen and carbon dioxide storage, and as “nano-reactors” for small molecules. However, little is known about the behaviour of reactive species in such materials. We have employed muon spin spectroscopy to characterize various organic free radicals which reside as isolated guests in structure II clathrates. The radicals are formed by reaction of atomic muonium (Mu) with the guest molecules: furan and two isomeric dihydrofurans. Muonium is essentially a light isotope of hydrogen, and adds to unsaturated molecules in the same manner as H. We have determined muon and proton hyperfine coupling constants for the muoniated radicals formed in the clathrates and also in neat liquids at the same temperature. DFT calculations were used to guide the spectral assignments and distinguish between competing radical products for Mu addition to furan and 2,3-dihydrofuran. Relative signal amplitudes provide yields and thus the relative reactivities of the C4 and C5 addition sites in these molecules. Spectral features, hyperfine constants and reactivities all indicate that the radicals do not tumble freely in the clathrate cages in the same way that they do in liquids. &nbsp

Investigation of H atom and free radical behaviour in clathrate hydrates of organic molecules

Clathrate hydrates are icy materials composed of a lattice of water molecules containing well-defined cavities which can accommodate small guest molecules. Their large storage capacity makes clathrates attractive media for a variety of gas storage and separation applications, but there is relatively little information on the chemical stability and diffusion of guest molecules. At the fundamental level inter-cage transition energies have been calculated, but the results need to be tested with experimental data. Ideally this should involve single-atom transport, using an isotopic tracer or spin label. Muonium (Mu = µ+e–) qualifies on both counts. As a single-electron atom with the muon as nucleus it may be considered a light isotope of hydrogen. Furthermore muonium and its reaction products may be monitored by muon spin spectroscopy. In recent years we have used this method to probe H-atom and free radical behaviour in clathrate hydrates. The current work extends studies to benzene and acetone clathrate hydrates. Of note is the simultaneous detection of muonium and muoniated radicals in the same sample. This can happen when Mu is trapped in an empty cavity, remote from its reaction partner. Increase in temperature leads to transport of Mu between cages and results in encounters with reactive guest molecules. By studying the temperature dependence of Mu and radical signals, we have been able to determine the activation energy for transport of Mu between cavities

Free Radical Reactivity of a Phosphaalkene Explored Through Studies of Radical Isotopologues

Muonium (Mu), an H atom analogue, is employed to probe the addition of free radicals to the P=C bond of a phosphaalkene. Specifically, two unprecedented muoniated free radicals, MesP•-CMu(Me)2 (1a, minor product) and MesPMu-C•Me2 (1b, major product), were detected by muon spin spectroscopy (µSR) when a solution of MesP=CMe2 (1: Mes = 2,4,6-trimethylphenyl) was exposed to a beam of positive muons (µ+). The µ+ serves as a source of Mu (i.e. Mu = µ+ + e–). To confirm the identity of the major product 1b, its spectral features were compared to its isotopologue, MesPH-C•(Me)CH2Mu (2a). Conveniently, 2a is the sole product of the reaction of MesPH(CMe=CH2) (2) with Mu. For all observed radicals, muon, proton and phosphorus hyperfine coupling constants were determined by µSR and compared to DFT-calculated values

Exploring main group radicals using an isotope of hydrogen

Muonium, which is considered a light isotope of the H atom, is a radioactive atom with a lifetime of 2.197 µs. Muonium adds to unsaturated molecules to form muoniated radicals. The collection of spectroscopic techniques that are used to observe muoniated radicals are known as µSR. To determine the identity of the muoniated radicals, experimental hyperfine coupling constants (hfcs) of the muoniated radicals obtained from µSR techniques were compared with hfcs of the muoniated radicals calculated using Density Functional Theory (DFT) methods available in the Gaussian 09 software package. µSR studies help us understand the reactivity of molecules towards the H atom and the configuration and conformation of the radicals formed. The polyether ether ketone (PEEK) polymer was tested for suitability in µSR sample cell fabrication. Muoniated radicals formed from monomers of PEEK, 4,4-dihydroxybenzophenone and para-dimethoxybenzene were detected. Since similar radicals expected in PEEK could interfere with sample signals it is concluded that PEEK is unsuitable for µSR sample cells. Phosphaalkene reactions with muonium were studied to understand their behaviour in radical polymerization. The model compound mesPC(Me)2 was studied and two muoniated free radicals, mesP-MuC•(Me)2 and mesP•-C(Mu)Me2 were detected. The mesP•-C(Mu)Me2 radical was compared with its isotopologue mesPH-C•(Me)CH2Mu formed from mesPH(CMe=CH2). A number of phosphaalkenes that differ from each other with respect to electronegativity and the bulkiness of the attached substituent groups were studied. Adamantyl phosphaalkene (AdP=CtBuH) produced only the AdMuP-C•(tBuH) radical while a sample of (CF3)2-mesP=C(Me)2 showed muoniation at both the P and C centers of the P=C bond. Muoniated radicals formed by mesP=CPh2 were identified. This helped to resolve ambiguity in identifying the initiation products of the radical polymerization pathway of mesP=CPh2. The reaction of Mu with 2,4,6-tri-tert-butyl-1,3,5-triphosphosphabenzene (TPB) resulted in two muoniated radicals. Mu addition to the C atoms of the ring resulted in rearrangement to form a bicyclic product. TPB undergoes hydrogenation via a cationic route forming a bicyclic product. In this thesis I propose a radical route for this hydrogenation pathway.In summary we have utilized µSR techniques to broaden the understanding of neutral radical formation from phospha-organic compounds

Organic Free Radicals in Clathrate Hydrates Investigated by Muon Spin Spectroscopy

Very little is known about the behavior of free H atoms and small organic radicals inside clathrate hydrate structures despite the relevance of such species to combustion of hydrocarbon hydrates. Muonium is an H atom analog, essentially a light isotope of hydrogen, and can be used to probe the chemistry of H atoms and transient free radicals. We demonstrate the first application of muon spin spectroscopy to characterize radicals in clathrate hydrates. Atomic muonium was detected in hydrates of cyclopentane and tetrahydrofuran, and muoniated free radicals were detected in the hydrates of cyclopentene and 2,5-dihydrofuran, indicating rapid addition of muonium to the organic guest. Muon avoided level-crossing spectra of the radicals in hydrates are markedly different to those of the same radicals in pure organic liquids at the same temperature, and this can be explained by limited mobility of the enclathrated radicals, leading to anisotropy in the hyperfine interactions

Characterization of Free Radicals in Clathrate Hydrates of Furan, 2,3-Dihydrofuran, and 2,5-Dihydrofuran by Muon Spin Spectroscopy

In addition to their importance as abundant hydrocarbon deposits in nature, clathrate hydrates are being studied as potential media for hydrogen and carbon dioxide storage and as “nano-reactors” for small molecules. However, little is known about the behavior of reactive species in such materials. We have employed muon spin spectroscopy to characterize various organic free radicals that reside as isolated guests in structure II clathrates. The radicals are formed by reaction of atomic muonium (Mu) with the guest molecules furan and two isomeric dihydrofurans. Muonium is essentially a light isotope of hydrogen and adds to unsaturated molecules in the same manner as H. We have determined muon and proton hyperfine coupling constants for the muoniated radicals formed in the clathrates and also in neat liquids at the same temperature. DFT calculations were used to guide the spectral assignments and distinguish between competing radical products for Mu addition to furan and 2,3-dihydrofuran. Relative signal amplitudes provide yields and thus the relative reactivities of the C4 and C5 addition sites in these molecules. Spectral features, hyperfine constants, and reactivities all indicate that the radicals do not tumble freely in the clathrate cages in the same way that they do in liquids

N-Glycoproteome of E14.Tg2a Mouse Embryonic Stem Cells

E14.Tg2a mouse embryonic stem (mES) cells are a widely used host in gene trap and gene targeting techniques. Molecular characterization of host cells will provide background information for a better understanding of functions of the knockout genes. Using a highly selective glycopeptide-capture approach but ordinary liquid chromatography coupled mass spectrometry (LC-MS), we characterized the N-glycoproteins of E14.Tg2a cells and analyzed the close relationship between the obtained N-glycoproteome and cell-surface proteomes. Our results provide a global view of cell surface protein molecular properties, in which receptors seem to be much more diverse but lower in abundance than transporters on average. In addition, our results provide a systematic view of the E14.Tg2a N-glycosylation, from which we discovered some striking patterns, including an evolutionarily preserved and maybe functionally selected complementarity between N-glycosylation and the transmembrane structure in protein sequences. We also observed an environmentally influenced N-glycosylation pattern among glycoenzymes and extracellular matrix proteins. We hope that the acquired information enhances our molecular understanding of mES E14.Tg2a as well as the biological roles played by N-glycosylation in cell biology in general

Summary of highly represented protein classes in the N-glycoproteome derived from multiple annotation sources.

<p>The color of the nodes indicates different data sources. The size of the nodes and the width of the edges represent the number of proteins that are listed in the table or labeled in the figure, and the color depth of both the nodes and the edges represents the correspondent enrichment p values.</p

The number of predicted N-glycans and transmembrane (TM) domains based on protein sequences from listed species.

<p>Proteins are selected based on the sequence homology to the identified mouse proteins. Homology mapping is conducted NCBI HomoloGenes. Mouse: <i>Mus Musculus</i>; human: <i>Homo Sapiens</i>; fish: <i>Danio Rerio</i>; fly: <i>Drosophila Melanogaster</i>; worm: <i>Caenorhabditis Elegans</i>.</p