Post-acquisition ETD spectral processing for increased peptide identifications

Tandem mass spectra (MS/MS) produced using electron transfer dissociation (ETD) differ from those derived from collision-activated dissociation (CAD) in several important ways. Foremost, the predominant fragment ion series are different: c- and z ^·-type ions are favored in ETD spectra while b- and y-type ions comprise the bulk of the fragments in CAD spectra. Additionally, ETD spectra possess charge-reduced precursors and unique neutral losses. Most database search algorithms were designed to analyze CAD spectra, and have only recently been adapted to accommodate c- and z ^·-type ions; therefore, inclusion of these additional spectral features can hinder identification, leading to lower confidence scores and decreased sensitivity. Because of this, it is important to pre-process spectral data before submission to a database search to remove those features that cause complications. Here, we demonstrate the effects of removing these features on the number of unique peptide identifications at a 1% false discovery rate (FDR) using the open mass spectrometry search algorithm (OMSSA). When analyzing two biologic replicates of a yeast protein extract in three total analyses, the number of unique identifications with a ∼1% FDR increased from 4611 to 5931 upon spectral pre-processing—an increase of ∼28. 6%. We outline the most effective pre-processing methods, and provide free software containing these algorithms.     

Self-assembly of photonic crystals from polymer colloids

This article reviews recent developments in self-assembly of polymer colloids into colloidal crystals, a good candidate material for photonic crystals. Self-assembly strategy has developed as a facile and efficient method to fabricate colloidal crystals. Much research work has been focused on controlling the morphology and improving the quality, as well as finding applications of the colloidal crystals.     

Investigation of FeB alloy prepared by an electric arc method and used as the anode material for alkaline secondary batteries

High active FeB alloy was prepared by an electric arc method, and used as the anode material for alkaline secondary batteries. The structural characteristics of the as-prepared FeB alloy were studied using X-ray diffraction (XRD) and X-ray photoelectron spectroscopy (XPS), and the electrochemical performances were investigated using cyclic voltammetry (CV) and charge–discharge test. The FeB alloy achieves an excellent reversible capacity of 312 mA h/g as well as a good cycleability, and is proved to be a promising low-cost and high performance anode material for alkaline secondary batteries.     

Theoretical studies on electronic structures and spectroscopic properties of a series of novel β-diketonate Os(II) complexes

The geometries, electronic structures, and spectroscopic properties of a series of [Os^(II)(CO)₃(tfa)(acac(X)₂)] (tfa = trifluoroacetate; acac = acetoylacetonate; X = H (1), CF₃ (2), C₆H₅ (3), and C₁₀H₇ (4)) complexes have been investigated theoretically. The ground and excited state geometries were optimized at the B3LYP/LANL2DZ and CIS/LANL2DZ levels, respectively. The optimized geometry structural parameters agreed well with the corresponding experimental results. As indicated in this paper, the highest occupied molecular orbitals were dominantly localized on the Os atom, ctfa (abbv. of CO and tfa), and acac ligand for 1 and 2, acac ligand and X substituent for 3 and 4, while the lowest unoccupied molecular orbitals were mainly composed of acac ligand and X substituent. Under the time-dependent density functional theory (TDDFT) level with the polarized continuum model (PCM), the absorption and phosphorescence in CH₂Cl₂ media were calculated based on the optimized ground- and excited-state geometries, respectively. The calculated results show that the lowest energy absorptions at 317 (1), 342 (2), 377 (3), and 420 nm (4) are attributed to a change of ππ*/MLCT mixing transition to pure ππ* transition for 1–4, while their phosphorescence emission have similar transition properties. This indicates that the absorption and emission transition characters could be altered by adjusting the π electron-donating ability.     

Hydrogen‐Bond‐Selective Phase Transfer of Nanoparticles across Liquid/Gel Interfaces

In the swim : Colloidal nanoparticles coated with polylactide (PLA, red) and poly(ethylene glycol) brushes (PEG, black) can transfer from organic to aqueous phases across liquid/liquid or liquid/gel interfaces during degradation of the PLA coating (see picture: first step), which is driven selectively by the hydrogen bonding of the PEG coating with the aqueous phase (second step).

     

A study of the interaction between enantiomers of zolmitriptan and hydroxypropyl-beta-cyclodextrin by capillary electrophoresis

The enantioresolution of zolmitriptan was performed using cyclodextrin (CD)-modified capillary zone electrophoresis (CZE) with hydroxypropyl-β-CD (HP-β-CD) as the chiral selector. The influence of experimental conditions on the enantioseparation of zolmitriptan, such as pH, temperature, applied voltage, and concentrations of running electrolyte and CD, was systematically investigated, obtaining a baseline separation of two enantiomers by the use of a 25 mM sodium dihydrogen phosphate (SDPH) running electrolyte (pH 2.4) containing 30 mM HP-β-CD at 15 °C. Binding constants for each enantiomer–HP-β-CD pair at different temperatures, as well as thermodynamic parameters for binding, were calculated. A nonlinear van’t Hoff plot was obtained, indicating that the thermodynamic parameters of complexation were temperature-dependent for zolmitriptan enantiomers. The significant contribution of the enthalpy difference to the Gibbs free energy change suggested a stereomeric barrier mechanism for chiral recognition. Figure Resolution of zolmitriptan enantiomers was achieved by using CD-modified CZE Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Chiral ruthenium-SDPs/diamine complexes-catalyzed enantioselective hydrogenation of α-alkyl arylacetones via dynamic kinetic resolution

The asymmetric hydrogenation of the conformationally flexible racemic α-substituted acyclic dialkyl ketones via dynamic kinetic resolution (DKR) has been developed by using Ru-SDPs/diamine catalysts. Chiral alcohols were produced in high yields with good to excellent enantioselectivities (85%–97% ee) and diastereoselectivities (up to 97:3). This hydrogenation reaction provided a new approach to the synthesis of the key intermediate of J-104118.     

DFT evaluation of the electronic structures and spectroscopic properties of the self-assembled [Pt2M4(C ≡ CH)8] (M=Cu,Ag) clusters

Science China Chemistry - Electronic structures and spectroscopic properties of self-assembled [Pt2M4(C≡CH)8] (M=Cu, Ag) clusters have been studied by the TD-DFT (time-dependent density...     

Synthesis and Crystal Structure of [1,2,4]-Triazolo-annulated 3-Aza-A-homocholestane Derivative: A Novel Pentaheterocyclic Ring System

Abstract  

A novel pentaheterocyclic ring system derived from (5α)-cholestan-3-one, i.e. [1R-[1α(R*),3aβ,3bα,5aβ,12aα,12bβ,14aα]]-1-(1,5-dimethylhexyl)-1,2,3,3a,3b,4,5,11,12,12a,12b,13,14,14a-tetradecahydro-8,12a,14a-trimethyl-9-(2,4,6-trichlorophenyl)-cyclopenta[5,6]naphtho[2,1-d][1,2,4]triazolo[1,5-a]azepinium hexachloroantimonate (6) has been synthesized via the reverse-electron-demand 1,3-dipolar cycloaddition of the 1-aza-2-azoniaallene cation 4 to the triple bond of acetonitrile followed by ring enlargement. The structure of 6 was determined by NMR, IR and high-resolution mass spectra, and unequivocally confirmed by X-ray crystallographic analysis. The title compound crystallizes in monoclinic class under the space group P2-1 with a = 8.163(3) ?, b = 11.214(4) ?, c = 24.191(9) ?, α = 90°, β = 97.740(5)°, and γ = 90°. The five-membered triazole ring is essentially planar and aromatic, while the seven-membered azepine ring is not planar, but adopts a chair-like conformation.     

Synthesis,Crystal Structure and Luminescent Properties of One Silver Complex with 3,5-Diphenylpyrazole

Abstract  

A new Ag(I) complex Ag(HL)₂(NO₃) 1 has been synthesized with 3,5-diphenylpyrazole (HL) and characterized by IR spectrum, elemental analysis and X-ray crystallography. The crystallographic data for the complex 1: triclinic P[`\text1] P{\bar{\text{1}}} , a = 10.4369(17) ?, b = 10.4837(18) ?, c = 12.963(2) ?, α = 69.318(2)°, β = 86.733(3)°, γ = 88.263(2)°, V = 1324.7(4) ?³, Z = 2, Dc = 1.530 Mg m⁻³, F(000) = 620, μ = 0.803 mm⁻¹, R ₁ = 0.0251, wR ₂ = 0.0638. Ag(I) atom is bound to two nitrogen atoms from two ligands. In solid state there are π···π interactions and C–H···π interactions between adjacent units to generate 2D supramolecular structure. The title complex shows strong luminescent emission at 389 and 467 nm in solid state at room temperature.