On the benefits of acquiring peptide fragment ions at high measured mass accuracy

The advantages and disadvantages of acquiring tandem mass spectra by collision-induced dissociation (CID) of peptides in linear ion trap Fourier-transform hybrid instruments are described. These instruments offer the possibility to transfer fragment ions from the linear ion trap to the FT-based analyzer for analysis with both high resolution and high mass accuracy. In addition, performing CID during the transfer of ions from the linear ion trap (LTQ) to the FT analyzer is also possible in instruments containing an additional collision cell (i.e., the "C-trap" in the LTQ-Orbitrap), resulting in tandem mass spectra over the full m/z range and not limited by the ejection q value of the LTQ. Our results show that these scan modes have lower duty cycles than tandem mass spectra acquired in the LTQ with nominal mass resolution, and typically result in fewer peptide identifications during data-dependent analysis of complex samples. However, the higher measured mass accuracy and resolution provides more specificity and hence provides a lower false positive ratio for the same number of true positives during database search of peptide tandem mass spectra. In addition, the search for modified and unexpected peptides is greatly facilitated with this data acquisition mode. It is therefore concluded that acquisition of tandem mass spectral data with high measured mass accuracy and resolution is a competitive alternative to "classical" data acquisition strategies, especially in situations of complex searches from large databases, searches for modified peptides, or for peptides resulting from unspecific cleavages.     

A forced march across an RNA folding landscape

In a recent issue of Science, Greenleaf et al. (2008) report single-molecule force measurements to explore the sequential folding landscape of an adenine riboswitch aptamer domain. This study provides an exceptionally quantitative view of how an RNA molecule folds.     

Protein identification via ion-trap collision-induced dissociation and examination of low-mass product ions

A whole-protein tandem mass spectrometry approach for protein identification based on precursor ion charge state concentration via ion/ion reactions, ion-trap collisional activation, ion/ion proton-transfer reactions involving the product ions, and mass analysis over a narrow m/z range (up to m/z 2000) is described and evaluated. The experiments were carried out with a commercially available electrospray ion-trap instrument that has been modified to allow for ion/ion reactions. Reaction conditions and the approach to searching protein databases were developed with the assumption that the resolving power of the mass analyzer is insufficient to distinguish charge states on the basis of the isotope spacings. Ions derived from several charge states of cytochrome c, myoglobin, ribonuclease A, and ubiquitin were used to evaluate the approach for protein identification and to develop a two-step procedure to database searching to optimize specificity. The approach developed with the model proteins was then applied to whole cell lysate fractions of Saccharomyces cerevisiae. The results are illustrated with examples of assignments made for three a priori unknown proteins, each selected randomly from a lysate fraction. Two of the three proteins were assigned to species present in the database, whereas one did not match well any database entry. The combination of the mass measurement and the product ion masses suggested the possibility for the oxidation of two methionine residues of a protein in the database. The examples show that this limited whole-protein characterization approach can provide insights that might otherwise be lacking with approaches based on complete enzymatic digestion.     

Rapid formation of metal-organic nano-capsules gives new insight into the self-assembly process

Metal-organic pyrogallol[4]arene nano-capsules, mixed pyrogallol[4]arene nano-capsules, and mixed metal analogues have been rapidly synthesised by addition of excess copper nitrate to a methanol solution of the corresponding macrocycle(s) (or gallium nano-capsules for the mixed metal system); improved solubility allows for thorough study and elucidation of the assembly process for these discrete metal-organic assemblies.     

Selection rules and symmetry relations for four-wave mixing measurements of uniaxial assemblies

Uniaxial systems represent the next lowest symmetry below isotropic and are ubiquitous. The objective of the present work is to present a systematic foundation for interpreting polarization-dependent four-wave mixing measurements of oriented and aligned assemblies. Orientational averages connecting the molecular frame to the macroscopic frame in uniaxial assemblies were derived for several common molecular symmetry groups for coherent anti-Stokes Raman spectroscopy (CARS) measurements, coherent anti-Stokes two-photon spectroscopy (CATS) probing electronic transitions, resonant two-photon absorption (2PA), and traditional Raman measurements. First, the complete set of orientational averages connecting the molecular and macroscopic frames was compiled for the most general case of C1 molecular symmetry. Then, the orientational averages of a select few commonly occurring molecular symmetry groups (Cs, C2, C2v, and C3v) were explored in greater detail to illustrate the approach and to facilitate the interpretation of routine experimental measurements. One outcome of this analysis is the prediction of efficient electric dipole-allowed chiral-specific four-wave mixing in uniaxially oriented media.     

On the irreducibility of Hecke polynomials

Let be the characteristic polynomial of the th Hecke operator acting on the space of cusp forms of weight for the full modular group. We record a simple criterion which can be used to check the irreducibility of the polynomials . Using this criterion with some machine computation, we show that if there exists such that is irreducible and has the full symmetric group as Galois group, then the same is true of for each prime .

     

Xanthene-Based Nitric Oxide-Responsive Nanosensor for Photoacoustic Imaging in the SWIR Window

Shortwave infrared (SWIR) dyes are characterized by their ability to absorb light from 900 to 1400 nm, which is ideal for deep tissue imaging owing to minimized light scattering and interference from endogenous pigments. An approach to access such molecules is to tune the photophysical properties of known near-infrared dyes. Herein, we report the development of a series of easily accessible (three steps) SWIR xanthene dyes based on a dibenzazepine donor conjugated to thiophene ( SCR-1 ), thienothiophene ( SCR-2 ), or bithiophene ( SCR-3 ). We leverage the fact that SCR-1 undergoes a bathochromic shift when aggregated for in vivo studies by developing a ratiometric nanoparticle for NO ( rNP-NO ), which we employed to successfully visualize pathological levels of nitric oxide in a drug-induced liver injury model via deep tissue SWIR photoacoustic (PA) imaging. Our work demonstrates how easily this dye series can be utilized as a component in nanosensor designs for imaging studies.     

A Hemilabile NHC-Gold Complex and its Application to the Redox Neutral 1,2-Oxyarylation of Feedstock Alkenes

We describe a Au^I complex of a hemi-labile (C^N) N-heterocyclic carbene ligand that is able to mediate oxidative addition of aryl iodides. Detailed computational and experimental investigations have been undertaken to verify and rationalize the oxidative addition process. Application of this initiation mode has resulted in the first examples of “exogenous oxidant-free” Au^I/Au^III catalyzed 1,2-oxyarylations of ethylene and propylene. These demanding yet powerful processes establish these commodity chemicals as nucleophilic-electrophilic building blocks in catalytic reaction design.     

High-Spin and Reactive Fe13 Cluster with Exposed Metal Sites

Atomically defined large metal clusters have applications in new reaction development and preparation of materials with tailored properties. Expanding the synthetic toolbox for reactive high nuclearity metal complexes, we report a new class of Fe clusters, Tp*₄W₄Fe₁₃S₁₂ , displaying a Fe₁₃ core with M−M bonds that has precedent only in main group and late metal chemistry. M₁₃ clusters with closed shell electron configurations can show significant stability and have been classified as superatoms. In contrast, Tp*₄W₄Fe₁₃S₁₂ displays a large spin ground state of S=13. This compound performs small molecule activations involving the transfer of up to 12 electrons resulting in significant cluster rearrangements.     

Gas transport in TiO2 nanoparticle-filled poly(1-trimethylsilyl-1-propyne)

Titanium dioxide (TiO₂) nanoparticles were dispersed via solution processing in poly(1-trimethylsilyl-1-propyne) (PTMSP) to form nanocomposite films. Nanoparticle dispersion was investigated using atomic force microscopy and transmission electron microscopy. At low-particle loadings, nanoparticles were dispersed individually and in nanoscale aggregates. At high-particle loadings, some nanoparticles formed micron-sized aggregates. The gas transport and density exhibited a strong dependence on nanoparticle loading. At low-TiO₂ loadings, the composite density was similar to or slightly higher than that predicted by a two-phase additive model. However, at particle loadings exceeding approximately 7 nominal vol.%, the density was markedly lower than predicted, suggesting that the particles induced the creation of void space within the nanocomposite. For example, when the TiO₂ nominal volume fraction was 0.35, the polymer/particle composite density was 40% lower than expected based on a two-phase additive model for density. At low-nanoparticle loading, light gas permeability was lower than that of the unfilled polymer. At higher nanoparticle loadings, light gas permeability (i.e., CO₂, N₂, and CH₄) increased to more than four times higher than in unfilled PTMSP. At most, selectivity changed only slightly with particle loading.