A sample preparation method for recovering suppressed analyte ions in MALDI TOF MS

In matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI TOF MS), analyte signals can be substantially suppressed by other compounds in the sample. In this technical note, we describe a modified thin‐layer sample preparation method that significantly reduces the analyte suppression effect (ASE). In our method, analytes are deposited on top of the surface of matrix preloaded on the MALDI plate. To prevent embedding of analyte into the matrix crystals, the sample solution were prepared without matrix and efforts were taken not to re‐dissolve the preloaded matrix. The results with model mixtures of peptides, synthetic polymers and lipids show that detection of analyte ions, which were completely suppressed using the conventional dried‐droplet method, could be effectively recovered by using our method. Our findings suggest that the incorporation of analytes in the matrix crystals has an important contributory effect on ASE. By reducing ASE, our method should be useful for the direct MALDI MS analysis of multicomponent mixtures. Copyright © 2015 John Wiley & Sons, Ltd.     

Terminal Phosphanido Rhodium Complexes Mediating Catalytic PP and PC Bond Formation

Complexes with terminal phosphanido (M? PR₂) functionalities are believed to be crucial intermediates in new catalytic processes involving the formation of P? P and P? C bonds. We showcase here the isolation and characterization of mononuclear phosphanide rhodium complexes ([RhTp(H)(PR₂)L]) that result from the oxidative addition of secondary phosphanes, a reaction that was also explored computationally. These compounds are active catalysts for the dehydrocoupling of PHPh₂ to Ph₂P? PPh₂. The hydrophosphination of dimethyl maleate and the unactivated olefin ethylene is also reported. Reliable evidence for the prominent role of mononuclear phosphanido rhodium species in these reactions is also provided.     

Catalytic Synthesis of 8-Membered Ring Compounds via Cobalt(III)-Carbene Radicals

The metalloradical activation of o-aryl aldehydes with tosylhydrazide and a cobalt(II) porphyrin catalyst produces cobalt(III)-carbene radical intermediates, providing a new and powerful strategy for the synthesis of medium-sized ring structures. Herein we make use of the intrinsic radical-type reactivity of cobalt(III)-carbene radical intermediates in the [Co^II(TPP)]-catalyzed (TPP=tetraphenylporphyrin) synthesis of two types of 8-membered ring compounds; novel dibenzocyclooctenes and unprecedented monobenzocyclooctadienes. The method was successfully applied to afford a variety of 8-membered ring compounds in good yields and with excellent substituent tolerance. Density functional theory (DFT) calculations and experimental results suggest that the reactions proceed via hydrogen atom transfer from the bis-allylic/benzallylic C−H bond to the carbene radical, followed by two divergent processes for ring-closure to the two different types of 8-membered ring products. While the dibenzocyclooctenes are most likely formed by dissociation of o-quinodimethanes (o-QDMs) which undergo a non-catalyzed 8π-cyclization, DFT calculations suggest that ring-closure to the monobenzocyclooctadienes involves a radical-rebound step in the coordination sphere of cobalt. The latter mechanism implies that unprecedented enantioselective ring-closure reactions to chiral monobenzocyclooctadienes should be possible, as was confirmed for reactions mediated by a chiral cobalt-porphyrin catalyst.     

Snooker: a structure-based pharmacophore generation tool applied to class A GPCRs

G-protein coupled receptors (GPCRs) are important drug targets for various diseases and of major interest to pharmaceutical companies. The function of individual members of this protein family can be modulated by the binding of small molecules at the extracellular side of the structurally conserved transmembrane (TM) domain. Here, we present Snooker, a structure-based approach to generate pharmacophore hypotheses for compounds binding to this extracellular side of the TM domain. Snooker does not require knowledge of ligands, is therefore suitable for apo-proteins, and can be applied to all receptors of the GPCR protein family. The method comprises the construction of a homology model of the TM domains and prioritization of residues on the probability of being ligand binding. Subsequently, protein properties are converted to ligand space, and pharmacophore features are generated at positions where protein ligand interactions are likely. Using this semiautomated knowledge-driven bioinformatics approach we have created pharmacophore hypotheses for 15 different GPCRs from several different subfamilies. For the beta-2-adrenergic receptor we show that ligand poses predicted by Snooker pharmacophore hypotheses reproduce literature supported binding modes for ～75% of compounds fulfilling pharmacophore constraints. All 15 pharmacophore hypotheses represent interactions with essential residues for ligand binding as observed in mutagenesis experiments and compound selections based on these hypotheses are shown to be target specific. For 8 out of 15 targets enrichment factors above 10-fold are observed in the top 0.5% ranked compounds in a virtual screen. Additionally, prospectively predicted ligand binding poses in the human dopamine D3 receptor based on Snooker pharmacophores were ranked among the best models in the community wide GPCR dock 2010.     

On the “Tertiary Structure” of Poly‐Carbenes; Self‐Assembly of sp3‐Carbon‐Based Polymers into Liquid‐Crystalline Aggregates

The self‐assembly of poly(ethylidene acetate) (st‐PEA) into van der Waals‐stabilized liquid‐crystalline (LC) aggregates is reported. The LC behavior of these materials is unexpected, and unusual for flexible sp³‐carbon backbone polymers. Although the dense packing of polar ester functionalities along the carbon backbone of st‐PEA could perhaps be expected to lead directly to rigid‐rod behavior, molecular modeling reveals that individual st‐PEA chains are actually highly flexible and should not reveal rigid‐rod induced LC behavior. Nonetheless, st‐PEA clearly reveals LC behavior, both in solution and in the melt over a broad elevated temperature range. A combined set of experimental measurements, supported by MM/MD studies, suggests that the observed LC behavior is due to self‐aggregation of st‐PEA into higher‐order aggregates. According to MM/MD modeling st‐PEA single helices adopt a flexible helical structure with a preferred trans‐gauche syn‐syn‐anti‐anti orientation. Unexpectedly, similar modeling experiments suggest that three of these helices can self‐assemble into triple‐helical aggregates. Higher‐order assemblies were not observed in the MM/MD simulations, suggesting that the triple helix is the most stable aggregate configuration. DLS data confirmed the aggregation of st‐PEA into higher‐order structures, and suggest the formation of rod‐like particles. The dimensions derived from these light‐scattering experiments correspond with st‐PEA triple‐helix formation. Langmuir–Blodgett surface pressure–area isotherms also point to the formation of rod‐like st‐PEA aggregates with similar dimensions as st‐PEA triple helixes. Upon increasing the st‐PEA concentration, the viscosity of the polymer solution increases strongly, and at concentrations above 20 wt % st‐PEA forms an organogel. STM on this gel reveals the formation of helical aggregates on the graphite surface–solution interface with shapes and dimensions matching st‐PEA triple helices, in good agreement with the structures proposed by molecular modeling. X‐ray diffraction, WAXS, SAXS and solid state NMR spectroscopy studies suggest that st‐PEA triple helices are also present in the solid state, up to temperatures well above the melting point of st‐PEA. Formation of higher‐order aggregates explains the observed LC behavior of st‐PEA, emphasizing the importance of the “tertiary structure” of synthetic polymers on their material properties.     

Action of α-cyclodextrin on phospholipid assemblies

Interactions of α-cyclodextrin (α-CD) with dimyristoylphosphatidylcholine (DMPC) and Egg phosphatidylcholine (Egg-PC) were studied (i) by analyzing surface pressure-area isotherms and surface tension of phospholipid monolayers formed at the interface between air and α-CD aqueous solutions and (ii) by X-ray diffraction performed on fully hydrated α-CD/phospholipid binary mixtures. The cyclodextrin molecules strongly interact with the two-dimension phospholipid assembly. Their addition into the aqueous sub-phase leads to the removal of part of the phospholipids from the air-water interface: the higher the α-CD concentration, the higher the phospholipid depletion. This should preferentially involve interactions between cyclodextrin and the phosphatidylcholine head group as α-CD is water-soluble and not surface-active. At the three-dimension level, the bilayer packing of the phospholipid lamellar phase appears not affected by the presence of cyclodextrin as shown by X-ray scattering at small angles whereas wide-angle diffraction patterns reveal the formation of a crystalline phase organized in a pseudo-hexagonal lattice usually characteristic of α-CD dimers. These results point out that α-CD should interact with bilayer-forming phospholipid molecules but likely according to a process that would preserve intact at least a part of the multilamellar assembly.