Multidimensional nano-HPLC coupled with tandem mass spectrometry for analyzing biotinylated proteins

Multidimensional high-performance liquid chromatography (HPLC) is a key method in shotgun proteomics approaches for analyzing highly complex protein mixtures by complementary chromatographic separation principles. Here, we describe an integrated 3D-nano-HPLC/nano-electrospray ionization quadrupole time-of-flight mass spectrometry system that allows an enzymatic digestion of proteins followed by an enrichment and subsequent separation of the created peptide mixtures. The online 3D-nano-HPLC system is composed of a monolithic trypsin reactor in the first dimension, a monolithic affinity column with immobilized monomeric avidin in the second dimension, and a reversed phase C18 HPLC-Chip in the third dimension that is coupled to a nano-ESI-Q-TOF mass spectrometer. The 3D-LC/MS setup is exemplified for the identification of biotinylated proteins from a simple protein mixture. Additionally, we describe an online 2D-nano-HPLC/nano-ESI-LTQ-Orbitrap-MS/MS setup for the enrichment, separation, and identification of cross-linked, biotinylated species from chemical cross-linking of cytochrome c and a calmodulin/peptide complex using a novel trifunctional cross-linker with two amine-reactive groups and a biotin label.

Über Osmiumbromide

On Osmiumbromides OsBr₄ was obtained by reaction of OsCl₄ with bromine in a closed system at 330°C and 120 bar Br₂ pressure. The compound crystallizes orthorhombic (a = 633.99(18) pm; b = 1 210.92(16) pm; c = 1 461.5(10) pm; Z = 8; space group Pbca) in a TcCl₄ type structure. OsBr₆ octahedra are connected by two common edges to \documentclass{article}\pagestyle{empty}\begin{document}${}_\infty ^1 \left[ {{\rm OsBr}_{{{\rm 2} \mathord{\left/ {\vphantom {{\rm 2} 1}} \right. \kern-\nulldelimiterspace} 1}} {\rm Br}_{{{\rm 4} \mathord{\left/ {\vphantom {{\rm 4} 2}} \right. \kern-\nulldelimiterspace} 2}} } \right]$\end{document} chains with a cis arrangement of the two non-bridging Br atoms. Mixed crystals OsBr_xCl_4?x(0 < x < 2.3) with CsCl₄ type structure are formed by reactions at lower Br₂ pressure up to 12 bar. They are built up from chains consisting of edge-sharing octahedra. The terminal atoms have a trans arrangement. Attempts to synthesize single crystals of OsBr₃ by decomposition of OsBr₄ resulted in formation of three different phases OsBr_x (3 < x < 4).     

Essential oil extraction,chemical analysis and anti-Candida activity of Foeniculum vulgare Miller – new approaches

A comprehensive study on essential oil samples of Foeniculum vulgare Miller from Tarquinia (Italy) is reported. A 24-h systematic steam distillation was performed on different harvested samples applying different extraction times. The GC-MS analysis of the residue outcome showed o-cymene, α-phellandrene, α-pinene and estragole as the major constituents. The predominance and continued presence of o-cymene makes this fennel oil a rather unique chemotype. An evident correlation between the antifungal activity and phenological stage is demonstrated. The most active fractions were particularly rich in estragole, as well as a significant amount of fenchone that possibly exerts some additive effect in the expression of overall antifungal potency. Pre-fruiting material produced oil particularly rich in o-cymene. With reference to the duration of the extraction, the maximum amount of oil was released within the first 3 h, whereas the reproductive phase material needed at least 6 h for the extraction.     

Chemical promenades: Exploring potential-energy surfaces with immersive virtual reality

The virtual-reality framework AVATAR (Advanced Virtual Approach to Topological Analysis of Reactivity) for the immersive exploration of potential-energy landscapes is presented. AVATAR is based on modern consumer-grade virtual-reality technology and builds on two key concepts: (a) the reduction of the dimensionality of the potential-energy surface to two process-tailored, physically meaningful generalized coordinates, and (b) the analogy between the evolution of a chemical process and a pathway through valleys (potential wells) and mountain passes (saddle points) of the associated potential energy landscape. Examples including the discovery of competitive reaction paths in simple A + BC collisional systems and the interconversion between conformers in ring-puckering motions of flexible rings highlight the innovation potential that augmented and virtual reality convey for teaching, training, and supporting research in chemistry.     

Comprehensive model of electromigrative transport in microfluidic paper based analytical devices

A complete mathematical model for electromigration in paper-based analytical devices is derived, based on differential equations describing the motion of fluids by pressure sources and EOF, the transport of charged chemical species, and the electric potential distribution. The porous medium created by the cellulose fibers is considered like a network of tortuous capillaries and represented by macroscopic parameters following an effective medium approach. The equations are obtained starting from their open-channel counterparts, applying scaling laws and, where necessary, including additional terms. With this approach, effective parameters are derived, describing diffusion, mobility, and conductivity for porous media. While the foundations of these phenomena can be found in previous reports, here, all the contributions are analyzed systematically and provided in a comprehensive way. Moreover, a novel electrophoretically driven dispersive transport mechanism in porous materials is proposed. Results of the numerical implementation of the mathematical model are compared with experimental data, showing good agreement and supporting the validity of the proposed model. Finally, the model succeeds in simulating a challenging case of free-flow electrophoresis in paper, involving capillary flow and electrophoretic transport developed in a 2D geometry.     

Chalcogen–chalcogen-bond activation by an ambiphilic,doubly reduced organoborane

The 9,10-dimethyl-9,10-dihydro-9,10-diboraanthracene dianion salt Li₂[1] instantaneously reacts with the dichalcogens O₂(tBu)₂, S₂Me₂, S₂(pTol)₂, Se₂Ph₂, and Te₂Ph₂ under reductive cleavage of the chalcogen–chalcogen bonds to give lithium chalcogenides and neutral 1. In solution, the products are involved in rapid association/dissociation equilibria. In the crystalline state, 1 and Li[O(tBu)] form a diadduct, whereas Li[SMe] gives a B?B-bridged monoadduct. In the three remaining cases, the crystal lattices contain monoadducts of 1 with one tri- and one tetracoordinate boron atom.     

Detection and characterization of silver nanoparticles in chicken meat by asymmetric flow field flow fractionation with detection by conventional or single particle ICP-MS

A method of analysis of silver nanoparticles (AgNPs) in chicken meat was developed. The homogenized chicken meat sample, which was spiked with AgNPs, was subjected to enzymolysis by Proteinase K for 40 min at 37 °C. Transmission electron microscopy and inductively coupled plasma mass spectrometry (ICP-MS) in single particle mode were used to characterize the number-based size distribution of AgNPs in the meat digestate. Because similar size distributions were found in the meat digestate and in the aqueous suspension of AgNPs used for spiking the meat, it was shown that no detectable dissolution of the AgNPs took place during the sample preparation stage. The digestate was injected into the asymmetric flow field flow fractionation (AF⁴) -ICP-MS system, which enabled fractionation of nanoparticles from the remaining meat matrix, and resulted in one large peak in the fractograms as well as two smaller peaks eluting close to the void volume. The recovery of silver contained in the large AgNP peak was around 80 %. Size determination of AgNPs in the meat matrix, based on external size calibration of the AF⁴ channel, was hampered by non-ideal (early elution) behavior of the AgNPs. Single particle ICP-MS was applied for determination of the number-based particle size distribution of AgNPs in collected fractions. The presented work describes for the first time the coupling of AF⁴ and ICP-MS for AgNP separation in a food matrix.     

Unusual nitration of substituted 7-amino-1,8-naphthyridine in the synthesis of compounds with antiplatelet activity

Several 1,8-naphthyridine derivatives have been diazotizated to obtain the corresponding hydroxy derivatives or mixture of hydroxy and hydroxy nitro derivatives. The respective amounts of hydroxy and hydroxy nitro derivatives depends on the nature of the substituents, on their position on the naphthyridine nucleus, on the amount of sodium nitrite and on the reaction temperature. A study of the electronic density of some molecules suggests a possible explanation of the effects induced by the nature of the substituents and of their position. Some of the compounds were tested for their ability to inhibit human platelet aggregation in vitro induced by arachidonic acid. Only compound 26 showed interesting antiplatelet activity.     

Pre-organization of the core structure of E-selectin antagonists

A new class of N-acetyl-D-glucosamine (GlcNAc) mimics for E-selectin antagonists was designed and synthesized. The mimic consists of a cyclohexane ring substituted with alkyl substituents adjacent to the linking position of the fucose moiety. Incorporation into E-selectin antagonists led to the test compounds 8 and the 2'-benzoylated analogues 21, which exhibit affinities in the low micromolar range. By using saturation transfer difference (STD)-NMR it could be shown that the increase in affinity does not result from an additional hydrophobic contact of the alkyl substituent with the target protein E-selectin, but rather from a steric effect stabilizing the antagonist in its bioactive conformation. The loss of affinity found for antagonists 10 and 35 containing a methyl substituent in a remote position (and therefore unable to support to the stabilization of the core) further supports this hypothesis. Finally, when a GlcNAc mimetic containing two methyl substituents (52 and 53) was used, in which one methyl was positioned adjacent to the fucose linking position and the other was in a remote position, the affinity was regained.