High‐throughput workflow for identification of phosphorylated peptides by LC‐MALDI‐TOF/TOF‐MS coupled to in situ enrichment on MALDI plates functionalized by ion landing

We report an MS‐based workflow for identification of phosphorylated peptides from trypsinized protein mixtures and cell lysates that is suitable for high‐throughput sample analysis. The workflow is based on an in situ enrichment on matrix‐assisted laser desorption/ionization (MALDI) plates that were functionalized by TiO₂ using automated ion landing apparatus that can operate unsupervised. The MALDI plate can be functionalized by TiO₂ into any array of predefined geometry (here, 96 positions for samples and 24 for mass calibration standards) made compatible with a standard MALDI spotter and coupled with high‐performance liquid chromatography. The in situ MALDI plate enrichment was compared with a standard precolumn‐based separation and achieved comparable or better results than the standard method. The performance of this new workflow was demonstrated on a model mixture of proteins as well as on Jurkat cells lysates. The method showed improved signal‐to‐noise ratio in a single MS spectrum, which resulted in better identification by MS/MS and a subsequent database search. Using the workflow, we also found specific phosphorylations in Jurkat cells that were nonspecifically activated by phorbol 12‐myristate 13‐acetate. These phosphorylations concerned the mitogen‐activated protein kinase/extracellular signal‐regulated kinase signaling pathway and its targets and were in agreement with the current knowledge of this signaling cascade. Control sample of non‐activated cells was devoid of these phosphorylations. Overall, the presented analytical workflow is able to detect dynamic phosphorylation events in minimally processed mammalian cells while using only a short high‐performance liquid chromatography gradient. Copyright © 2015 John Wiley & Sons, Ltd.     

Structure and electronic properties of hollow‐caged C60 fullerene‐derived (MN4)nC6(10 − n) (M = Zn,Mg, Fe,n = 1−6) complexes

Unique hollow‐caged (MN₄)_nC_{6(10 ? n)} (M = Zn, Mg, Fe, n = 1?6) complexes designed by introduction of n porphyrinoid fragments in C₆₀ fullerene structure were proposed and the atomic and electronic structures were calculated using LC‐DFT MPWB95 and M06 potentials and 6‐311G(d)/6‐31G(d) basis sets. The complexes were optimized using various symmetric configurations from the highest O_h to the lowest C₁ point groups in different spin states from S = 0 (singlet) to S = 7 (quindectet) for M = Fe to define energetically preferable atomic and electronic structures. Several metastable complexes were determined and the key role of the metal ions in stabilization of the atomic structure of the complexes was revealed. For Fe₆N₂₄C₂₄, the minimum energy was reported for C_2h, D_2h, and D_4h symmetry of pentet state S = 2, so the complex can be regarded as unique molecular magnet. It was found that the metal partial density of states determine the nature of HOMO and LUMO levels making the clusters promising catalysts. © 2014 Wiley Periodicals, Inc.     

1,3-Bis(2-alkyltetrazol-5-yl)triazenes and their Fe(II), Co(II) and Ni(II) complexes: Synthesis,spectroscopy, and thermal properties. Crystal structure of Fe(II) and Co(II) 1,3-bis(2-methyltetrazol-5-yl)triazenide complexes

Complexes ML¹₂ and ML²₂, with M = Fe^II, Co^II, Ni^II, and 1,3-bis(2-R-tetrazol-5-yl)triazenide ligands L¹ (R = Me) and L² (R = ^tBu), have been synthesized by the reaction of corresponding 1,3-bis(2-R-tetrazol-5-yl)triazenes with metal(II) salts in basic media and characterized by IR, UV–Vis spectroscopy, thermal and X-ray diffraction analyses. Both 1,3-bis(2-R-tetrazol-5-yl)triazenes were found to deprotonate on coordination and act as tridentate chelating ligands forming distorted MN₆ octahedra around metal(II) cations.     

Micro-bore titanium housed polymer monoliths for reversed-phase liquid chromatography of small molecules

A new method for the fixation of polymethacrylate monoliths within titanium tubing of up to 0.8 mm I.D. for use as a chromatographic column under elevated temperatures and pressures is described. The preparation of butyl methacrylate–ethylene dimethacrylate-based monolithic stationary phases with desired porous structures was achieved within titanium tubing with pre-oxidised internal walls. The oxidised titanium surface was subsequently silanised with 3-trimethoxysilylpropyl methacrylate resulting in tight bonding of butyl methacrylate porous monolith to the internal walls, providing stationary phase stability at column temperatures up to 110 °C and at operating column pressure drops of >28 MPa. The titanium housed monoliths exhibited a uniform and dense porous structure, which provided peak efficiencies of up to 59,000 theoretical plates per meter when evaluated for the separation of small molecules in reversed-phase mode, under optimal conditions (achieved at 15 μL/min and temperature of 110 °C for naphthalene with a retention factor, k = 0.58). The developed column was applied to the reversed-phase isocratic separation of a text mixture of pesticides.     

Immobilization of porphyrins in poly(hydroxymethylsiloxane)

Three tetracationic porphyrins differing in the position of charged nitrogen atoms on the peripheral substituents — 5,10,15,20-tetrakis(N-methylpyridinium-4-yl)porphyrin (TMPyP4), 5,10,15,20-tetrakis(N-methylpyridinium-2-yl)porphyrin (TMPyP2), 5,10,15,20-tetrakis(4-trimethylammoniophenyl) porphyrin (TMAPP), and hydrophobic 5,10,15,20-tetraphenylporphyrin (TPP), were immobilized by adsorption and encapsulation in poly(hydroxymethylsiloxane) (PHOMS). The so prepared porphyrin-PHOMS composites were characterized by porosimetry, scanning electron microscopy, fluorescence and diffuse reflectance UV-VIS spectroscopy. It was found that porphyrins are immobilized in the PHOMS matrix in the free base monomer form Their irradiation produced singlet oxygen O₂(¹Δ_g) with the lifetime of 10–30 μs.     

Guidelines for the analysis of free energy calculations

Journal of Computer-Aided Molecular Design - Free energy calculations based on molecular dynamics simulations show considerable promise for applications ranging from drug discovery to prediction of...     

Stability constants of the Li+, Na+, H3O+, NH4+, Ag+, and K+ complexes of the cone conformer of tetraethyl p-tert-butyltetrathiacalix[4]arene tetraacetate in nitrobenzene saturated with water

Abstract  

From extraction experiments in the two-phase water–nitrobenzene system and γ-activity measurements, the stability constants of the tetraethyl p-tert-butyltetrathiacalix[4]arene tetraacetate (cone)·M⁺ complexes (M⁺ = Li⁺, H₃O⁺, NH₄ ⁺, Ag⁺, or K⁺) were determined in water-saturated nitrobenzene. It was found that these constants increase in the cation order NH₄ ⁺ < K⁺ < H₃O⁺ < Ag⁺ < Li⁺ < Na⁺.     

Biosynthesis of Quantum Dots (CdTe) and its Effect on Eisenia fetida and Escherichia coli

Biosynthesis belongs to one of the new possibilities of nanoparticles preparation, whereas its main advantage is biocompatibility. In addition, the ability of obtaining the raw material for such synthesis from the soil environment is beneficial and could be useful for remediation. However, the knowledge of mechanisms that are necessary for the biosynthesis or effect on the bio-synthesizing organisms is still insufficient. In this study, we attempted to evaluate the effect of quantum dots (QDs) not only on a model organism of collembolans, but also on another soil organism—earthworm Eisenia fetida—and in also one widespread microorganism such as Escherichia coli. Primarily, we determined 28EC₅₀ as 72.4 μmol L^?1 for CdTe QDs in collembolans. Further, we studied the effect of QDs biosynthesis in E. fetida and E. coli. Using determination of QDs, low-molecular thiols and antioxidant activities, we found differences between both organisms and also between ways how they behave in the presence of Cd and/or Cd and Te. The biosynthesis in earthworms can be considered as its own protective mechanism; however, in E. coli, it is probably a by-product of protective mechanisms.     

Ferromagnetically Coupled S=1 Chains in Crystals of Verdazyl-Nitronyl Nitroxide Diradicals

Thermally stable organic diradicals with a triplet ground state along with large singlet-triplet energy gap have significant potential for advanced technological applications. A series of phenylene-bridged diradicals with oxoverdazyl and nitronyl nitroxide units were synthesized via a palladium-catalyzed cross-coupling reaction of iodoverdazyls with a nitronyl nitroxide-2-ide gold(I) complex with high yields. The diradicals exhibit high stability and do not decompose in an inert atmosphere up to 180 °C. For the diradicals, both substantial AF (ΔE_ST≈−64 cm⁻¹) and FM (ΔE_ST≥25 and 100 cm⁻¹) intramolecular exchange interactions were observed. The sign of the exchange interaction is determined both by the bridging moiety (para- or meta-phenylene) and by the type of oxoverdazyl block (C-linked or N-linked). Upon crystallization, diradicals with the triplet ground state form unique one-dimensional exchange-coupled chains with strong intra- and weak inter-diradical ferromagnetic coupling.