An automated high performance capillary liquid chromatography-Fourier transform ion cyclotron resonance mass spectrometer for high-throughput proteomics

We describe a fully automated high performance liquid chromatography 9.4 tesla Fourier transform ion resonance cyclotron (FTICR) mass spectrometer system designed for proteomics research. A synergistic suite of ion introduction and manipulation technologies were developed and integrated as a high-performance front-end to a commercial Bruker Daltonics FTICR instrument. The developments incorporated included a dual-ESI-emitter ion source; a dual-channel electrodynamic ion funnel; tandem quadrupoles for collisional cooling and focusing, ion selection, and ion accumulation, and served to significantly improve the sensitivity, dynamic range, and mass measurement accuracy of the mass spectrometer. In addition, a novel technique for accumulating ions in the ICR cell was developed that improved both resolution and mass measurement accuracy. A new calibration methodology is also described where calibrant ions are introduced and controlled via a separate channel of the dual-channel ion funnel, allowing calibrant species to be introduced to sample spectra on a real-time basis, if needed. We also report on overall instrument automation developments that facilitate high-throughput and unattended operation. These included an automated version of the previously reported very high resolution, high pressure reversed phase gradient capillary liquid chromatography (LC) system as the separations component. A commercial autosampler was integrated to facilitate 24 h/day operation. Unattended operation of the instrument revealed exceptional overall performance: Reproducibility (1-5% deviation in uncorrected elution times), repeatability (<20% deviation in detected abundances for more abundant peptides from the same aliquot analyzed a few weeks apart), and robustness (high-throughput operation for 5 months without significant downtime). When combined with modulated-ion-energy gated trapping, the dynamic calibration of FTICR mass spectra provided decreased mass measurement errors for peptide identifications in conjunction with high resolution capillary LC separations over a dynamic range of peptide peak intensities for each spectrum of 10(3), and >10(5) for peptide abundances in the overall separation.     

Carbamidocyclophanes F and G with anti-Mycobacterium tuberculosis activity from the cultured freshwater cyanobacterium Nostoc sp.

Two new (1 and 2) and three known (3–5) carbamidocyclophanes were isolated from a cultured freshwater cyanobacterium Nostoc sp. (UIC 10274) obtained from a sample collected at Des Plaines, Illinois. Their planar structures and stereoconfigurations were determined by extensive spectroscopic analysis including 1D/2D NMR experiments, HRESIMS as well as CD spectroscopy. Carbamidocyclophane F (1) showed potent anti-Mycobacterium tuberculosis activity in the microplate Alamar blue assay and low-oxygen-recovery assay with MIC values of 0.8 and 5.4 μM, respectively. Carbamidocyclophane F (1) also displayed antimicrobial activities against the gram positive bacteria Staphylococcus aureus and Enterococcus faecalis with MIC values of 0.1 and 0.2 μM, respectively. Carbamidocyclophane F (1) and Carbamidocyclophane G (2) both showed antiproliferative activity against MDA-MB-435 and HT-29 human cancer cell lines with IC₅₀ values in the range from 0.5 to 0.7 μM.     

Proteasome-inhibitory and cytotoxic constituents of Garcinia lateriflora: absolute configuration of caged xanthones

A new biflavonoid (1), a new xanthone enantiomer (2), five new caged xanthones (3-7), and several known compounds were isolated from the stem bark of Garcinia lateriflora, collected in Indonesia. The structures of the new compounds were determined by analysis of spectroscopic data, and the absolute configuration of the caged xanthones was shown for the first time at carbons 5, 7, 8, 8a, 10a, and 27, by analysis of COSY and NOESY NMR and ECD spectra. The biflavonoids exhibited proteasome-inhibitory activity, and the known compound, morelloflavone (8) was found to have the greatest potency (IC₅₀=1.3 μM). The caged xanthones were cytotoxic toward HT-29 cells, with the known compound, morellic acid (10) being the most active (ED₅₀=0.36 μM). However, when tested in an in vivo hollow fiber assay, it was inactive at the highest dose tested (20 mg/kg).     

Gold-catalyzed rearrangement of substituted allyl aryl ethers

Triphenylphosphinegold(I) complexes catalyze the Claisen-type rearrangement of aryl allyl ethers to the corresponding branched and linear products. The product distribution depends on the olefin geometry of the allylic ether. Stereochemical transfer experiments support an ionic mechanism.     

A Synthetic Pathway to Cys-Xxx-Cys (N2S2) Analogue Ligands: An Improved Synthesis of HSCH2CH2C(O)NHCH2C(O)NHCH2CH2SH

Herein, two improved synthetic pathways to biologically relevant Cys-Xxx-Cys analogue ligands used in conjunction with metals as metalloenzyme models (Ni for carbon monoxide dehydrogenase/acetyl-CoA synthase A-cluster; Co and Fe for nitrile hydratase) are reported.     

Using force-matching to reveal essential differences between density functionals in ab initio molecular dynamics simulations

The exchange-correlation (XC) functional and value of the electronic fictitious mass μ can be two major sources of systematic errors in ab initio Car-Parrinello Molecular Dynamics (CPMD) simulations, and have a significant impact on the structural and dynamic properties of condensed-phase systems. In this work, an attempt is made to identify the origin of differences in liquid water properties generated from CPMD simulations run with the BLYP and HCTH∕120 XC functionals and two different values of μ (representative of "small" and "large" limits) by analyzing the effective pairwise atom-atom interactions. The force-matching (FM) algorithm is used to map CPMD interactions into non-polarizable, empirical potentials defined by bonded interactions, pairwise short-ranged interactions in numerical form, and Coulombic interactions via atomic partial charges. The effective interaction models are derived for the BLYP XC functional with μ=340 a.u. and μ=1100 a.u. (BLYP-340 and BLYP-1100 simulations) and the HCTH∕120 XC functional with μ=340 a.u. (HCTH-340 simulation). The BLYP-340 simulation results in overstructured water with slow dynamics. In contrast, the BLYP-1100 and HCTH-340 simulations both produce radial distribution functions (indicative of structure) that are in reasonably good agreement with experiment. It is shown that the main difference between the BLYP-340 and HCTH-340 effective potentials arises in the short-ranged nonbonded interactions (in hydrogen bonding regions), while the difference between the BLYP-340 and BLYP-1100 interactions is mainly in the long-ranged electrostatic components. Collectively, these results demonstrate how the FM method can be used to further characterize various simulation ensembles (e.g., density-functional theory via CPMD). An analytical representation of each effective interaction water model, which is easy to implement, is presented.     

A Mild and Regioselective Route to Functionalized Quinazolines

A Rh‐catalyzed ortho‐amidation cyclocondensation sequence gave a range of 4‐aminoquinazolines in high yield. The method features a remarkably mild C(sp²)?H activation step and can be exploited to rapidly access compounds with established biological activity.     

The Characterization of a Neutron Radiography Triga Reactor for NAA of Chlorine in an Iron Oxide Matrix

An irradiation position in the 250 kW Triga reactor was characterized for instrumental neutron activation analysis of chlorine in an iron oxide matrix. Factors that affect the accuracy of the determination include variations in the reactor neutron spectrum and flux as a function of spatial position and the presence of chlorine impurities. Gold wire and foils were used to determine the neutron flux and cadmium ratio as a function of height in an air-filled irradiation tube.     

Luminescence Characterization of a Novel, Hydrophobically Modified and Heavy Atom-Functionalized, Water-Soluble Polymer

A hydrophobically modified water-soluble polymer, based upon acrylic acid and styryl derivatives, was synthesized. A proportion (ca. 75 mol%) of the styryl residues in the copolymer contain a bromine substituent as a heavy-atom functionality. It has been shown that room-temperature phosphorescence (RTP) can be induced in an acenaphthylene (ACE) label, covalently bound to the polymer chain, through intramacromolecular interactions in dilute solutions of the copolymer. This is the first instance in which RTP has been generated in either label or solubilized guest, in such a fashion. The conformational behavior of the functionalized copolymer, BrSTY/STY/AA, has been studied using RTP, fluorescence lifetime, and time-resolved anisotropy measurements and compared to that of both its unbrominated, styrene-modified analogue, STY/AA, and poly(acrylic acid) PAA itself. The conformation transition which accompanies conversion of each polyacid into the corresponding fully neutralized polysalt is much more dramatic in either hydrophobically modified species than in poly(acrylic acid). Intramacromolecular aggregation leading to the creation of hydrophobic domains within the coils of the macromolecules is enhanced at a low pH and severely impedes segmental motion in the two styrene-modified polyacids. The effect is greater in the bromine-containing polymer, which suggests that more densely packed domains are formed in this species than in STY/AA. In addition to altering the magnitude of the effect that neutralization has upon the molecular dynamics of the polyacid in aqueous media, hydrophobic modification raises the pH range over which the change in conformational behavior of the macromolecule is apparent.