Fragmentation trees for the structural characterisation of metabolites

Metabolite identification plays a crucial role in the interpretation of metabolomics research results. Due to its sensitivity and widespread implementation, a favourite analytical method used in metabolomics is electrospray mass spectrometry. In this paper, we demonstrate our results in attempting to incorporate the potentials of multistage mass spectrometry into the metabolite identification routine. New software tools were developed and implemented which facilitate the analysis of multistage mass spectra and allow for efficient removal of spectral artefacts. The pre-processed fragmentation patterns are saved as fragmentation trees. Fragmentation trees are characteristic of molecular structure. We demonstrate the reproducibility and robustness of the acquisition of such trees on a model compound. The specificity of fragmentation trees allows for distinguishing structural isomers, as shown on a pair of isomeric prostaglandins. This approach to the analysis of the multistage mass spectral characterisation of compounds is an important step towards formulating a generic metabolite identification method. Copyright ? 2012 John Wiley & Sons, Ltd.     

Covalent attachment of antagonists to the α7 nicotinic acetylcholine receptor: synthesis and reactivity of substituted maleimides

The 3-methylmaleimide congeners of the natural product methyllycaconitine (MLA) and an analogue covalently attach to functional cysteine mutants of the α7 nicotinic acetylcholine receptor (nAChR).     

Spanning trees without adjacent vertices of degree 2

Albertson, Berman, Hutchinson, and Thomassen showed in 1990 that there exist highly connected graphs in which every spanning tree contains vertices of degree 2. Using a result of Alon and Wormald, we show that there exists a natural number $d$ such that every graph of minimum degree at least $d$ contains a spanning tree without adjacent vertices of degree 2. Moreover, we prove that every graph with minimum degree at least 3 has a spanning tree without three consecutive vertices of degree 2.     

Chemical Bonding in Colossal Thermopower FeSb2

FeSb₂ exhibits a colossal Seebeck coefficient ( ) and a record-breaking high thermoelectric power factor. It also has an atypical shift from diamagnetism to paramagnetism with increasing temperature, and the fine details of its electron correlation effects have been widely discussed. The extraordinary physical properties must be rooted in the nature of the chemical bonding, and indeed, the chemical bonding in this archetypical marcasite structure has been heavily debated on a theoretical basis since the 1960s. The two prevalent models for describing the bonding interactions in FeSb₂ are based on either ligand-field stabilization of Fe or a network structure of Sb hosting Fe ions. However, neither model can account for the observed properties of FeSb₂. Herein, an experimental electron density study is reported, which is based on analysis of synchrotron X-ray diffraction data measured at 15 K on a minute single crystal to limit systematic errors. The analysis is supplemented with density functional theory calculations in the experimental geometry. The experimental data are at variance with both the additional single-electron Sb−Sb bond implied by the covalent model, and the large formal charge and expected d-orbital splitting advocated by the ionic model. The structure is best described as an extended covalent network in agreement with expectations based on electronegativity differences.     

Self-Assembly of DNA–Peptide Supermolecules: Coiled-Coil Peptide Structures Templated by d-DNA and l-DNA Triplexes Exhibit Chirality-Independent but Orientation-Dependent Stabilizing Cooperativity

DNA nanostructures have been designed and used in many different applications. However, the use of nucleic acid scaffolds to promote the self-assembly of artificial protein mimics is only starting to emerge. Herein five coiled-coil peptide structures were templated by the hybridization of a d -DNA triplex or its mirror-image counterpart, an l -DNA triplex. The self-assembly of the desired trimeric structures in solution was confirmed by gel electrophoresis and small-angle X-ray scattering, and the stabilizing synergy between the two domains was found to be chirality-independent but orientation-dependent. This is the first example of using a nucleic acid scaffold of l -DNA to template the formation of artificial protein mimics. The results may advance the emerging POC-based nanotechnology field by adding two extra dimensions, that is, chirality and polarity, to provide innovative molecular tools for rational design and bottom-up construction of artificial protein mimics, programmable materials and responsive nanodevices.     

Chemical Causes of Metal Nobleness

Humans have appreciated the “noble” metals for millennia, yet modern chemistry still struggles with different definitions. Herein, metal nobleness is analyzed using thermochemical cycles including the different bulk, gas, and solution states implied by these definitions. The analysis suggests that metal nobleness mainly reflects inability to fulfil the electron demands of electronegative oxygen. Accordingly, gold is the most noble metal in existence, not because of d-band properties of the solid state, but because gold's electronegativity is closest to that of oxygen, producing weaker polar covalent bonding. The high electronegativity arises from the effective nuclear charge due to diffuse d-states, enforced by relativistic effects. This explanation accounts for the activity series, corrosion tendency, and trends in oxygen chemisorption, which other models do not. While gold is the most noble metal, the ranking of Ag, Pt, and Pd depends on the thermochemistry as discussed in detail.     

Strain and defect densities in Si/Si1-xGex heterostructures investigated by ion scattering and X-ray diffraction

MBE-grown Si/Si_1-xGe_x heterostructures on (100) Si have been characterized by Rutherford backscattering spectroscopy (RBS), ion channeling and X-ray diffraction to investigate defect densities and tetragonal lattice distortion. Critical layer thickness and relaxation of strain by formation of misfit dislocations are strongly dependent on the growth temperature. A Si_0.67Ge_0.33 layer with a thickness of 2000 Å is found to be still fully strained at a growth temperature of 450°C, whereas the same layer grown at 550°C shows considerable strain relaxation by dislocations. To obtain better depth resolution than with conventional RBS, medium energy ion scattering (MEIS) experiments have been performed on Si/Ge superlattices with layer thicknesses of 10–40 Å. A position-sensitive toroidal electrostatic analyser was employed to detect the backscattered ions simultaneously over an angular range of 30° with an energy resolution of 1 keV FWHM for 250 keV He ions, corresponding to a depth resolution of about 10 Å.     

Production of π0 mesons and charged hadrons in\bar v neon and ν neon charged current interactions

The average multiplicities of charged hadrons and of π⁺, π^? and π⁰ mesons, produced in \(\bar v\) Ne and νNe charged current interactions in the forward and backward hemispheres of theW ^±-nucleon center of mass system, are studied with data from BEBC. The dependence of the multiplicities on the hadronic mass (W) and on the laboratory rapidity (y _Lab) and the energy fraction (z) of the pion is also investigated. Special care is taken to determine the π⁰ multiplicity accurately. The ratio of average π multiplicities \(\frac{{2\left\langle {n_{\pi ^O } } \right\rangle }}{{[\left\langle {n_{\pi ^ + } } \right\rangle + \left\langle {n_{\pi ^ - } } \right\rangle ]}}\) is consistent with 1. In the backward hemisphere \(\left\langle {n_{\pi ^O } } \right\rangle \) is positively correlated with the charged multiplicity. This correlation, as well as differences in multiplicities between \(\mathop v\limits^{( - )} \) and \(\mathop v\limits^{( - )} \) , \(\mathop v\limits^{( - )} \) scattering, is attributed to reinteractions inside the neon nucleus of the hadrons produced in the initial \(\mathop v\limits^{( - )} \) interaction.     

Dry Chemistry of Ferrate(VI): A Solvent‐Free Mechanochemical Way for Versatile Green Oxidation

The +6 oxidation state of iron generally exists in the form of ferrate(VI) with high redox potential and environmentally friendly nature. Although ferrate(VI) has been known for over a century, its chemistry is still limited to the solvent‐based reactions that suffers from the insolubility/instability of this oxidant and the environmental issues caused by hazardous solvents. Herein, we explore the solvent‐free reactivity of ferrate(VI) under mechanical milling, revealing that its strong oxidizing power is accessible in the “dry” solid state towards a broad variety of substrates, for example, aromatic alcohols/aldehydes and carbon nanotubes. More significantly, solvent‐free mechanochemistry also reshapes the oxidizing ability of ferrate(VI) due to the underlying solvent‐free effect and the promotive mechanical actions. This study opens up a new chemistry of ferrate(VI) with promising application in green oxidative transformation of both organic and inorganic substrates.