Autopiquer - a Robust and Reliable Peak Detection Algorithm for Mass Spectrometry

We present a simple algorithm for robust and unsupervised peak detection by determining a noise threshold in isotopically resolved mass spectrometry data. Solving this problem will greatly reduce the subjective and time-consuming manual picking of mass spectral peaks and so will prove beneficial in many research applications. The Autopiquer approach uses autocorrelation to test for the presence of (isotopic) structure in overlapping windows across the spectrum. Within each window, a noise threshold is optimized to remove the most unstructured data, whilst keeping as much of the (isotopic) structure as possible. This algorithm has been successfully demonstrated for both peak detection and spectral compression on data from many different classes of mass spectrometer and for different sample types, and this approach should also be extendible to other types of data that contain regularly spaced discrete peaks.

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Realistic sampling of amino acid geometries for a multipolar polarizable force field

The Quantum Chemical Topological Force Field (QCTFF) uses the machine learning method kriging to map atomic multipole moments to the coordinates of all atoms in the molecular system. It is important that kriging operates on relevant and realistic training sets of molecular geometries. Therefore, we sampled single amino acid geometries directly from protein crystal structures stored in the Protein Databank (PDB). This sampling enhances the conformational realism (in terms of dihedral angles) of the training geometries. However, these geometries can be fraught with inaccurate bond lengths and valence angles due to artefacts of the refinement process of the X‐ray diffraction patterns, combined with experimentally invisible hydrogen atoms. This is why we developed a hybrid PDB/nonstationary normal modes (NM) sampling approach called PDB/NM. This method is superior over standard NM sampling, which captures only geometries optimized from the stationary points of single amino acids in the gas phase. Indeed, PDB/NM combines the sampling of relevant dihedral angles with chemically correct local geometries. Geometries sampled using PDB/NM were used to build kriging models for alanine and lysine, and their prediction accuracy was compared to models built from geometries sampled from three other sampling approaches. Bond length variation, as opposed to variation in dihedral angles, puts pressure on prediction accuracy, potentially lowering it. Hence, the larger coverage of dihedral angles of the PDB/NM method does not deteriorate the predictive accuracy of kriging models, compared to the NM sampling around local energetic minima used so far in the development of QCTFF. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

Synthesis of Meso‐Substituted Subphthalocyanine–Subporphyrin Hybrids: Boron Subtribenzodiazaporphyrins

The first syntheses of hybrid structures that lie between subphthalocyanines and subporphyrins are reported. The versatile single‐step synthetic method uses a preformed aminoisoindolene to provide the bridging methine unit and its substituent while trialkoxyborates simultaneously act as Lewis acid, template, and provider of the apical substituent. The selection of each component therefore allows for the controlled formation of diverse, differentially functionalized systems. The new hybrids are isolated as robust, pure materials that display intense absorption and emission in the mid‐visible region. The new compounds are further characterized in solution and solid state by variable‐temperature NMR spectroscopy and X‐ray crystallography, respectively.     

A new route for the synthesis of phosphate esters: 2,2′‐[benzene‐1,2‐diylbis(oxy)]bis(5,5‐dimethyl‐1,3,2‐dioxaphosphinane) 2,2′‐dioxide

Podand‐type ligands are an interesting class of acyclic ligands which can form host–guest complexes with many transition metals and can undergo conformational changes. Organic phosphates are components of many biological molecules. A new route for the synthesis of phosphate esters with a retained six‐membered ring has been used to prepare 2,2′‐[benzene‐1,2‐diylbis(oxy)]bis(5,5‐dimethyl‐1,3,2‐dioxaphosphinane) 2,2′‐dioxide, C₆H₄{O[cyclo‐P(O)OCH₂CMe₂CH₂O]}₂ or C₁₆H₂₄O₈P₂, (1), 2‐[(2′‐hydroxybiphenyl‐2‐yl)oxy]‐5,5‐dimethyl‐1,3,2‐dioxaphosphinane 2‐oxide, [cyclo‐P(O)OCH₂CMe₂CH₂O](2,2′‐OC₆H₄–C₆H₄OH), (2), and oxybis(5,5‐dimethyl‐1,3,2‐dioxaphosphinane) 2,2′‐dioxide, O[cyclo‐P(O)OCH₂CMe₂CH₂O]₂, (3). Compound (1) is novel, whereas the results for compounds (2) and (3) have been reported previously, but we record here our results for compound (3), which we find are more precise and accurate than those currently reported in the literature. In (1), two cyclo‐P(O)OCH₂CMe₂CH₂O groups are linked through a catechol group. The conformations about the two catechol O atoms are quite different, viz. one C—C—O—P torsion angle is −169.11 (11)° and indicates a trans arrangement, whereas the other C—C—O—P torsion angle is 92.48 (16)°, showing a gauche conformation. Both six‐membered POCCCO rings have good chair‐shape conformations. In both the trans and gauche conformations, the catechol O atoms are in the axial sites and the short P=O bonds are equatorially bound.     

Enhancement of electron-capture detection of methyl bromide in air by iodination.

An instrumentally simple and cost-effective method for the direct analysis of methyl bromide in ambient air is described. The method is based on the separation of sample components by gas chromatography, the conversion of methyl bromide to methyl iodide by reaction with an inorganic iodide salt, and the detection of the methyl iodide thereby produced by an electron-capture detector. Of the 20 different inorganic salts investigated here for conversion of methyl bromide to methyl iodide, zinc iodide was found to provide the greatest conversion efficiency. In addition, zinc iodide was found to provide high conversion efficiency at a modest reaction temperature, thereby minimizing both the thermal decomposition of compounds within the reaction volume and the level of column bleed introduced to the detector. The reactions of several other brominated and chlorinated organic compounds with zinc iodide have also been characterized. The successful application of this instrument to the quantitative determination of methyl bromide in a local background air sample is then demonstrated.     

Anomalous stability of aqueous boehmite dispersions induced by hydrolyzed aluminium poly-cations

Aqueous dispersions of colloidal boehmite rods turn into strong gels when the concentration of (1–1) electrolyte concentrations becomes exceeds 50 mM. However, after addition of aluminium chlorohydrate (ACH) the rods remain stable up to salt concentrations as high as 2 M. Moreover the boehmite-ACH dispersions with an aspect ratio of 19 quickly separate into an isotropic and a liquid crystal nematic phase above a typical threshold concentration of 2 v/v%. It is known that ACH forms polynuclear cations at mild acidic conditions. The anomalous stability as encountered in these dispersions is explained by assuming that these hydrolyzed poly-cations cause a shift of the charge carrying surface.     

Pulsed laser spectroscopy in muonium and deuterium

The 1s–2s energy interval in the muonium (μ⁺e⁻) atom has been measured by Doppler free two photon laser spectroscopy. A value of 2455528941.0(9.8) MHz has been obtained in good agreement with quantum electrodynamics (QED). The muon-electron mass ratio can be extracted and is found to be 206.76838(17). The measurement may also be interpreted as a determination of the muon-electron charge ratio as -1- 1.1(2.1)· 10⁻⁹. Corresponding measurements in deuterium using the same experimental setup confirmed the validity of the applied analysis procedure. This revised version was published online in August 2006 with corrections to the Cover Date.     

Depth of modular invariant rings

It is well-known that the ring of invariants associated to a non-modular representation of a finite group is Cohen-Macaulay and hence has depth equal to the dimension of the representation. For modular representations the ring of invariants usually fails to be Cohen-Macaulay and computing the depth is often very difficult. In this paper¹ we obtain a simple formula for the depth of the ring of invariants for a family of modular representations. This family includes all modular representations of cyclic groups. In particular, we obtain an elementary proof of the celebrated theorem of Ellingsrud and Skjelbred [6].     

Novel effects produced on a two dimensional electron gas by introducing InAs dots in the plane of the quantum well

We show that the presence of InAs dots embedded in a host GaAs quantum well containing a two-dimensional electron gas dramatically modifies the cyclotron resonance (CR). Far-infrared CR measurements show two modes with different dispersions with applied magnetic field B. The lower-frequency mode, with a sub-linear dependence on B, is identified as a CR at low B, developing into a skipping orbit around the dot perimeters at higher B. This has not been previously observed for a system with randomly distributed scatterers. The higher-frequency mode is identified as a magnetoplasmon localised by the confining effect of the arrays of repulsive potentials due to the dots in the well.