Optimization of the design and operation of FAIMS analyzers

Field asymmetric waveform ion mobility spectrometry (FAIMS) holds significant promise for post-ionization separations in conjunction with mass-spectrometric analyses. However, a limited understanding of fundamentals of FAIMS analyzers has made their design and operation largely an empirical exercise. Recently, we developed an a priori simulation of FAIMS that accounts for both ion diffusion (including anisotropic components) and Coulomb repulsion, and validated it by extensive comparisons with FAIMS/MS data. Here it is corroborated further by FAIMS-only measurements, and applied to explore how key instrumental parameters (analytical gap width and length, waveform frequency and profile, the identity and flow speed of buffer gas) affect FAIMS response. We find that the trade-off between resolution and sensitivity can be managed by varying gap width, RF frequency, and (in certain cases) buffer gas, with equivalent outcome. In particular, the resolving power can be approximately doubled compared to "typical" conditions. Throughput may be increased by either accelerating the gas flow (preferable) or shortening the device, but below certain minimum residence times performance deteriorates. Bisinusoidal and clipped-sinusoidal waveforms have comparable merit, but switching to rectangular waveforms would improve resolution and/or sensitivity. For any waveform profile, the ratio of two between voltages in high and low portions of the cycle produces the best performance.     

How to choose one-dimensional basis functions so that a very efficient multidimensional basis may be extracted from a direct product of the one-dimensional functions: energy levels of coupled systems with as many as 16 coordinates

In this paper we propose a scheme for choosing basis functions for quantum dynamics calculations. Direct product bases are frequently used. The number of direct product functions required to converge a spectrum, compute a rate constant, etc., is so large that direct product calculations are impossible for molecules or reacting systems with more than four atoms. It is common to extract a smaller working basis from a huge direct product basis by removing some of the product functions. We advocate a build and prune strategy of this type. The one-dimensional (1D) functions from which we build the direct product basis are chosen to satisfy two conditions: (1) they nearly diagonalize the full Hamiltonian matrix; (2) they minimize off-diagonal matrix elements that couple basis functions with diagonal elements close to those of the energy levels we wish to compute. By imposing these conditions we increase the number of product functions that can be removed from the multidimensional basis without degrading the accuracy of computed energy levels. Two basic types of 1D basis functions are in common use: eigenfunctions of 1D Hamiltonians and discrete variable representation (DVR) functions. Both have advantages and disadvantages. The 1D functions we propose are intermediate between the 1D eigenfunction functions and the DVR functions. If the coupling is very weak, they are very nearly 1D eigenfunction functions. As the strength of the coupling is increased they resemble more closely DVR functions. We assess the usefulness of our basis by applying it to model 6D, 8D, and 16D Hamiltonians with various coupling strengths. We find approximately linear scaling.     

Novel "Potentially antiaromatic", acidichromic quinonediimines with tunable delocalization of their 6 pi-electron subunits

We present a novel family of "potentially antiaromatic" alkyl-substituted p-benzoquinonediimine pH-dependent chromophores. It appears from the structural data that these overall 12 pi-electron molecules should be better considered as constituted by two chemically connected but electronically not conjugated 6 pi-electron subunits. Molecule 5 appears to be the first example of two separated, conjugated, and localized 6 pi-electron systems that can be tuned by reversible protonation to become delocalized. The mono- and diprotonated derivatives have been characterized by spectroscopic methods and X-ray diffraction. These systems develop supramolecular interactions in the solid state that clearly reflect the degree of protonation and depend on the nature of the counterion. These compounds constitute new chromophores for which the color can be tuned depending on the degree of protonation, going in solution from yellow for 5 to red for 5.HCl and blue for 5.2HCl. Theoretical calculations have provided a deeper insight into the electronic structure of these molecules and allowed an assignment of the experimental UV-vis spectra. The visible and near-UV spectrum of the neutral and protonated benzoquinonediimines can be classically assigned from the coupling of two 6 pi-electron polymethine units. TD-DFT calculations confirm the observed red shift of the two lowest pi --> pi* transitions of the benzoquinonediimines upon protonation and relate it to the moderate energy lowering of the HOMO --> LUMO transition induced by the delocalization of the polymethine pi system.     

Preparation of quinoxalines, dihydropyrazines, pyrazines and piperazines using tandem oxidation processes

Alpha-hydroxyketones undergo MnO2-mediated oxidation followed by in situ trapping with aromatic or aliphatic 1,2-diamines to give quinoxalines or dihydropyrazines, respectively, in a one pot procedure which avoids the need to isolate the highly reactive 1,2-dicarbonyl intermediates. Modifications of the procedure allow the formation of pyrazines and piperazines.     

An efficient,regio- and stereoselective palladium-catalyzed route to tetrasubstituted olefins

An efficient, regio- and stereoselective palladium-catalyzed route to tetrasubstituted olefins has been developed, which involves the intermolecular coupling of an aryl iodide, an internal alkyne, and an arylboronic acid. The reaction involves cis-addition of the aryl group from the aryl halide to the less hindered or less electron-poor end of the alkyne, while the aryl group from the arylboronic acid adds to the other end. [reaction: see text]     

A one-pot synthesis to [(Me3Si)3SiSb]4; a potential precursor for Sb42-

The reaction of (Me(3)Si)(3)SiK[middle dot]18-crown-6 with SbCl(3)(3 : 1 equiv.) provides a simple route to the title complex [(Me(3)Si)(3)SiSb](4). The potassium base initially acts as a nucleophile and then as a coupling agent, forming Sb-Sb bonds.     

Comparisons of NMR spectral quality and success in crystallization demonstrate that NMR and X-ray crystallography are complementary methods for small protein structure determination

X-ray crystallography and NMR spectroscopy provide the only sources of experimental data from which protein structures can be analyzed at high or even atomic resolution. The degree to which these methods complement each other as sources of structural knowledge is a matter of debate; it is often proposed that small proteins yielding high quality, readily analyzed NMR spectra are a subset of those that readily yield strongly diffracting crystals. We have examined the correlation between NMR spectral quality and success in structure determination by X-ray crystallography for 159 prokaryotic and eukaryotic proteins, prescreened to avoid proteins providing polydisperse and/or aggregated samples. This study demonstrates that, across this protein sample set, the quality of a protein's [15N-1H]-heteronuclear correlation (HSQC) spectrum recorded under conditions generally suitable for 3D structure determination by NMR, a key predictor of the ability to determine a structure by NMR, is not correlated with successful crystallization and structure determination by X-ray crystallography. These results, together with similar results of an independent study presented in the accompanying paper (Yee, et al., J. Am. Chem. Soc., accompanying paper), demonstrate that X-ray crystallography and NMR often provide complementary sources of structural data and that both methods are required in order to optimize success for as many targets as possible in large-scale structural proteomics efforts.     

1,8-Naphthyridines. Part III. Synthesis of some 6-substituted-1,8-naphthyridin-2(1H)ones

The syntheses of some 1,8-naphthyridines substituted in the 6-position with heterocyclic groups are described. A synthetic route to 6-amino-5,7-dimethyl-1,8-naphthyridin-2(1H)one is also presented.     

Selection of terms for a CI wavefunction to preserve potential surface features

A cumulative selection procedure for choosing configuration functions for inclusion in CI calculations is described. The objective of the method is to obtain equal energy loss, relative to unselected calculations, for different states and different regions of the potential surface. Results obtained from calculations on the BH molecule indicate an overall advantage in comparison to the threshold selection procedure, particularly with regard to molecular geometry changes.     

Application of solid phase microextraction in the determination of paralytic shellfish poisoning toxins

A SPME-HPLC-post-column fluorescent derivatization method for the direct determination of saxitoxin (STX), the most potent paralytic shellfish poisoning (PSP) toxin, in water has been developed. Commercially available SPME devices with 50 microm Carbowax templated resin (CW/TPR) coating was found to be able to pre-concentrate STX from aqueous media. A special pre-conditioning treatment of soaking the SPME coating in 0.1 M NaOH solution significantly improved the extraction efficiency. The optimal pH for the SPME process is 8.1 and the equilibration time is 40 min. The partition coefficient, K, of the distribution of STX between the SPME coating and the aqueous media was measured to be 2.99 +/- 0.04 x 10(3). Extracted toxin on the SPME stationary phase was difficult to be desorbed by the HPLC mobile phase under dynamic desorption mode. A static ion-pairing desorption technique using a desorption solvent mixture of 20 mM sodium 1-heptanesulfonate in 30% aqueous acetonitrile acidified with 50 mM sulfuric acid was developed to overcome this problem. The method detection limit and repeatability achieved by this SPME-HPLC method were 0.11 ng ml(-1) and 3.7%, respectively, with a sample volume of just 5 ml of water. This analytical method is adequate for the monitoring of the PSP toxin in fresh/drinking waters. However, serious interference was observed when this technique was applied to saline water samples. This is probably due to competition of sodium ions with the cationic STX for absorption into the SPME stationary phase.