Automated assignment of charge states from resolved isotopic peaks for multiply charged ions

The recent proliferation of electrospray as an ionization method has greatly increased the ability to perform analyses of large biomolecules by using mass spectrometry. The major advantage of electrospray is the ability to produce multiply charged ions, which brings large molecules down to a mass-to-charge ratio range amenable to most instruments. Multiple charging is also a disadvantage because mass (m) becomes ambiguous unless charge (z) can be assigned. This is typically performed with simple algorithms that use multiple peaks of the same m and different z, but these methods are difficult to apply to complex mixtures and not applicable when only one z appears for each m. The use of mass analyzers with higher resolving powers, like the Fourier transform mass spectrometer, allows resolution of isotopic peaks, providing an internal 1-Da mass scale that can be used for unambiguous charge assignment. Manual assignment of charge state from the isotopic peaks is time consuming and becomes inaccurate when either the signal level or resolving power are low. For these cases, computer algorithms based on pattern recognition techniques have been developed to assist in assignment of charge states to isotopic clusters. These routines provide for more rapid analysis with higher accuracy than available manually.     

Synthetic applications of aryl radical building blocks for cyclisation onto azoles

2-(2-Bromophenyl)ethyl groups have been used as building blocks in radical cyclisation reactions onto azoles to synthesise tri- and tetra-cyclic heterocycles. 2-(2-Bromophenyl)ethyl methanesulfonate was used to alkylate azoles (imidazoles, pyrroles, indoles and pyrazoles) for the synthesis of the radical precursors. Cyclisations of the intermediate aryl radicals yield new 6-membered rings attached to the azoles. The aryl radicals undergo intramolecular homolytic aromatic substitution onto the azole rings. Tributylgermanium hydride has been used with success to replace the toxic and troublesome tributyltin hydride. Initial studies show that the protocol can be used on solid phase resins. The molecular and crystal structures of methyl 5,6-dihydroimidazo[5,1-a]iso-quinoline-1-carboxylate and methyl 5,6-dihydroimidazo[2,1-a]isoquinoline-3-carboxylate were determined by X-ray crystallography.     

Formation and stability of N-heterocyclic carbenes in water: the carbon acid pKa of imidazolium cations in aqueous solution

We report second-order rate constants kDO (M-1 s-1) for exchange for deuterium of the C(2)-proton of a series of simple imidazolium cations to give the corresponding singlet imidazol-2-yl carbenes in D2O at 25 degrees C and I = 1.0 (KCl). Evidence is presented that the reverse protonation of imidazol-2-yl carbenes by solvent water is limited by solvent reorganization and occurs with a rate constant of kHOH = kreorg = 10(11) s-1. The data were used to calculate reliable carbon acid pK(a)s for ionization of imidazolium cations at C(2) to give the corresponding singlet imidazol-2-yl carbenes in water: pKa = 23.8 for the imidazolium cation, pKa = 23.0 for the 1,3-dimethylimidazolium cation, pKa = 21.6 for the 1,3-dimethylbenzimidazolium cation, and pKa = 21.2 for the 1,3-bis-((S)-1-phenylethyl)benzimidazolium cation. The data also provide the thermodynamic driving force for a 1,2-hydrogen shift at a singlet carbene: K12 = 5 x 10(16) for rearrangement of the parent imidazol-2-yl carbene to give neutral imidazole in water at 298 K, which corresponds to a favorable Gibbs free energy change of 23 kcal/mol. We present a simple rationale for the observed substituent effects on the thermodynamic stability of N-heterocyclic carbenes relative to a variety of neutral and cationic derivatives that emphasizes the importance of the choice of reference reaction when assessing the stability of N-heterocyclic carbenes.     

Evaluation of multidimensional (ion-exchange/reversed-phase) protein separations using linear and step gradients in the first dimension

The performance characteristics of multidimensional liquid chromatographic protein separations were evaluated using on-line electrospray mass detection, and a novel workflow for automated LC/MS data processing. Two-dimensional ion exchange/reversed-phase LC separations of Escherichia coli cytosol were conducted using either a continuous linear or discontinuous step gradient in the first dimension. Chromatographic profiles of the top 100 most abundant components were characterized to assess overall separation reproducibility within each mode, and to characterize differences in component distribution between the two modes of operation. Analysis of the resulting data indicates that multidimensional separations of complex protein mixtures can be done reproducibly. Furthermore, under the conditions employed within this study, a linear first dimension gradient was more effective at fractionating the protein mixture, distributing fewer major components to multiple second dimension cycles than an equivalent step gradient. The application of on line mass spectrometry, and automated processing of the resulting data, proved valuable for producing component level analysis of multidimensional protein separations.     

On-chip electrochromatography using sol-gel immobilized stationary phase with UV absorbance detection

A chromatography column on a chip was fabricated by immobilizing reversed-phase stationary phase particles (5 microm, C4) using sol-gel technology. Channels were fabricated in quartz using photolithography and wet etching. Localization of the stationary phase was achieved by immobilizing the stationary phase at the desired location in the separation channel prior to bonding of the cover plate. Cross channel design was employed for gated injection. An optical fiber setup was developed for carrying out on-chip UV absorbance detection. The effective optical path length was theoretically determined for the trapezoidal shaped channel and the result was shown to match closely with the experimentally determined value. The effect of applied voltage on velocity was evaluated using thiourea as an unretained marker. Separation performance of the stationary phase was demonstrated by separation of three peptides (Trp-Ala, Leu-Trp and Trp-Trp) under isocratic chromatographic conditions.     

Fully automated polymer-assisted synthesis of 1,5-biaryl pyrazoles

The polymer-assisted solution-phase (PASP) synthesis of a 192-member 2-D array of 1,5-biaryl pyrazoles 4[1-12,1-16] is reported. The synthesis was performed in a fully automated manner using a multiprobe top-filtration robot and incorporates a "catch and release" step to afford library compounds directly in high yield and purity.     

Hydrodynamics of a bounded vertical film with nonlinear surface properties

The drainage of a thin liquid film with an insoluble monolayer down a vertical wall is studied. Lubrication theory is used to develop a model where the film is pinned at the top with a given thickness and the film drains into a bath at the bottom. A nonlinear equation of state is used for the surface tension and the surface viscosity is a nonlinear function of the surfactant concentration; these are appropriate for some aqueous systems. The three partial differential equations are solved via discretization in space and then the resulting differential algebraic system is solved. Results are described for a wide range of parameters, and the conditions under which the free surface is immobilized are discussed.     

The heats of reaction of phosphines and phosphites with toluene-molybdenum tricarbonyl. Importance of both steric and electronic factors in determining the Mo---PR3 bond strength

The heats of reaction of tolueneMo(CO)₃ with a series of phosphines and phosphites have been measured by solution calorimetry. The order of stability toward formation of fac-(PR₃)₃Mo(CO)₃ in THF solution is: P(OCH₃)₃s> PMe₃ > PⁿBu₃ > PMe₂Ph> PEt₃ > triphos> P(OPh)₃ > PMePh₂ > PPh₃ > PCl₃ and spans a range of 25 kcal/mol reflecting individual bond strength differences up to 8 kcal/mol. The bulky phosphines PCy₃ and P^tBu₃ react with tolueneMo(CO)₃ in THF, but 30–40 kcal/mol less heat is evolved in these reactions than with the other phosphines and phosphites. The coordinately unsaturated five-coordinate complexes (PR₃)₂Mo(CO)₃ are proposed as the reaction products. The importance of both steric and electronic factors in the Mo---P bond is discussed.     

Poly(choloyl)-based amphiphiles as pore-forming agents: transport-active monomers by design

This paper describes the design and synthesis of a family of pore-forming amphiphiles. Two of these amphiphiles, which are derived from cholic acid, lysine, and p-phenylenediamine, can produce pores in lipid bilayers as individual molecules. In sharp contrast, analogous amphiphiles that do not contain a rigid 1,4-phenylenediamide moiety favor the formation of dimer-based pores. Kinetic evidence in support of monomer- and dimer-based pores has been obtained from Na+ transport measurements across bilayers made from 1-palmitoyl-2-oleoyl-2-sn-glycero-3-phosphocholine (POPC). Structure-activity studies that have been carried out with pore-forming, dimer-based amphiphiles have also revealed a significant activity dependence on their overall compactness. The practical potential of pore-forming amphiphiles with controllable supramolecular properties is briefly discussed.