Can density functional theory (DFT) be used as an aid to a deeper understanding of tandem mass spectrometric fragmentation pathways?

Prediction of tandem mass spectrometric (MS/MS) fragmentation for non‐peptidic molecules based on structure is of immense interest to the mass spectrometrist. If a reliable approach to MS/MS prediction could be achieved its impact within the pharmaceutical industry could be immense. Many publications have stressed that the fragmentation of a molecular ion or protonated molecule is a complex process that depends on many parameters, making prediction difficult. Commercial prediction software relies on a collection of general heuristic rules of fragmentation, which involve cleaving every bond in the structure to produce a list of ‘expected’ masses which can be compared with the experimental data. These approaches do not take into account the thermodynamic or molecular orbital effects that impact on the molecule at the point of protonation which could influence the potential sites of bond cleavage based on the structural motif. A series of compounds have been studied by examining the experimentally derived high‐resolution MS/MS data and comparing it with the in silico modelling of the neutral and protonated structures. The effect that protonation at specific sites can have on the bond lengths has also been determined. We have calculated the thermodynamically most stable protonated species and have observed how that information can help predict the cleavage site for that ion. The data have shown that this use of in silico techniques could be a possible way to predict MS/MS spectra. Copyright © 2009 John Wiley & Sons, Ltd.     

Determination of As,Cd, Pb,and Hg in urine using inductively coupled plasma mass spectrometry with the direct injection high efficiency nebulizer

The application of the large-bore direct injection high efficiency nebulizer (LB-DIHEN) for the determination of arsenic (As), cadmium (Cd), lead (Pb), and mercury (Hg) in urine by inductively coupled plasma mass spectrometry (ICP-MS) is described. The LB-DIHEN is compared with the standard method using a concentric pneumatic nebulizer and cyclonic spray chamber. In addition to the toxicological significance of As, Cd, Pb, and Hg, these elements represent a cross-section of analytical issues including spectral interferences (e.g., ⁴⁰Ar³⁵Cl⁺ on ⁷⁵As⁺ and ⁹⁸Mo¹⁶O⁺ on ¹¹⁴Cd⁺) and memory effects (Hg). In this study, the low sample consumption of the LB-DIHEN is used to reduce the volume of urine needed for analysis, and to reduce the volume of final diluted sample required for analysis. Eliminating the spray chamber and reducing the dead volume of the nebulizer reduces memory effects, especially for analytes such as Hg. The Dynamic Reaction Cell (DRC) is used in this study to attenuate the background level of ArCl⁺ in spite of the increase in the solvent load and, in turn, the urine matrix (chloride) delivered to the plasma by the LB-DIHEN. This is the first report on coupling the LB-DIHEN to a standard autosampler for unattended sample analysis. The robustness of direct injection nebulization for routine analysis and the issues associated with automation of the sample introduction process are discussed. Although the figures of merit (sensitivity, limit of detection, and precision) determined for both nebulizers are slightly poorer for the LB-DIHEN than for the concentric pneumatic nebulizer, there is not a clinically significant difference between the results for both sample introduction systems. The accuracy of results is assessed using archived urine materials that are circulated by several different proficiency testing (PT) programs and external quality assessment schemes (EQAS). Results obtained using the LB-DIHEN were within the acceptable range established by a consensus pool generated using different methods, none of which are likely to be using direct injection nebulization. Internal quality control sample results obtained using the LB-DIHEN were compared to those obtained using the conventional nebulizer. Reported results were similar for both nebulizers. Thus, these results show that the LB-DIHEN is certainly feasible for the analysis of urine specimens.     

Things That are Right with the Traditional Square of Opposition

The truth conditions that Aristotle attributes to the propositions making up the traditional square of opposition have as a consequence that a particular affirmative proposition such as ‘Some A is not B’ is true if there are no Bs. Although a different convention than the modern one, this assumption remained part of centuries of work in logic that was coherent and logically fruitful.      

Photophysics and X-ray structure of crystalline 2-aminopurine.

To explore the effect of intermolecular interactions on the photophysics of 2-aminopurine (2AP) in a well-defined environment, we have investigated the fluorescence properties of single 2AP crystals, having determined their X-ray structure. In the crystal, 2AP is subject to base-stacking and hydrogen-bonding interactions similar to those found in DNA. The crystal shows dual fluorescence: pi-stacked molecules in the bulk of the lattice have redshifted excitation and emission spectra, while molecules at defect sites have spectra similar to those of 2AP in solution or in DNA. Heterogeneous intermolecular interactions in the crystal give rise to multiexponential fluorescence decay characteristics similar to those observed for 2AP-labelled DNA. The presence of about 13 % of the 7H tautomer in the crystal confirms that 9H-7H tautomerisation of 2AP occurs in the ground state. Long-wavelength excitation of a 2AP-labelled oligonucleotide duplex produced redshifted emission similar to that observed in the crystal, indicating that pi-stacking interaction of 2AP with nucleobases gives rise to a low energy excited state.     

A New Synthesis of Charge‐Neutral Tris‐Pyrazolyl and ‐Methimazolyl Borate Ligands

The dimethylamine in the adducts [(HNMe₂)B(azolyl)₃] (azolyl=methimazolyl, pyrazolyl), obtained by reaction of the azole with B(NMe₂)₃, can readily be substituted with a range of nitrogen donors to provide new charge‐neutral, tripodal ligands in high yield. This observation has led to a revision of an earlier interpretation of the mechanism of the formation of these species. The donor properties of the ligands [(nmi)B(azolyl)₃] (nmi=N‐methylimidazole) have been compared with their anionic analogues [HB(azolyl)₃]^? by synthesis of their manganese(I)–tricarbonyl complexes and comparison of their infrared ν_CO energies. This comparison indicates that the new neutral ligands are only marginally weaker donors than the corresponding anionic hydrotris(azolyl)borate ligands. This may be explained by the ability of the attached nmi ring to stabilize a positive charge remotely from the coordinated metal, which may also account for the fact that the [(nmi)B(pyrazolyl)₃] ligand is a substantially stronger donor than the similarly neutral tris(pyrazolyl)methane ligand.     

A study of the removal of selenite and selenate from aqueous solutions using a magnetic iron/manganese oxide nanomaterial and ICP-MS

Selenium (Se) is naturally occurring in the environment and is an essential nutrient in mammals. However, environmental Se can be increased to toxic levels through different industrial practices. The potential adsorption of the Se oxoanions, selenite and selenate, from aqueous solutions onto nanosynthesized MnFe₂O₄ was investigated using batch techniques and DRC-ICP-MS spectroscopy. The nanomaterial (NM) was laboratory synthesized through slow titration of a mixture of Fe²⁺ and Mn²⁺ ions. X-ray diffraction and Scherrer's equation were used to determine the phase of the material and crystallite size, respectively. The effects of pH, reaction time, competitive anions, and the adsorption capacity of the synthesized NM to bind selenite and selenate were investigated. The Langmuir isotherm was used to determine the binding capacity of the NM. Results showed that the phase of the nanomaterial was similar to Jacobsite with a size of 27.5 nm. Results also showed that the sorption of either 100 ppb of selenite or selenate was pH independent in the pH range 2 to 6 and occurred within 5 min of contact time. The introduction of Cl⁻ and NO₃⁻ anions individually added to solution had no significant effect on the sorption of either selenite or selenate. However, it was found that the addition of SO₄²⁻ had a competitive effect only on the sorption of selenate, first seen at 10 ppm and more pronounced at 100 ppm of SO₄²⁻. In the presence of 100 ppm of PO₄³⁻, the adsorption of selenate decreased to 87% while selenite sorption decreased to 20%. From the Langmuir isotherm equation it was determined that the nano-Jacobsite had a selenite and selenate binding capacity of 6573.76 and 769.23 mg Se/kg of NM, respectively.     

Synthesis,Crystal Structure,and Rotational Energy Profile of 3-Cyclopropyl-1,2,4-benzotriazine 1,4-Di-<Emphasis Type="Italic">N</Emphasis>-oxide

Abstract  

1,2,4-Benzotriazine 1,4-di-N-oxides are potent antitumor drug candidates that undergo in vivo bioreduction leading to selective DNA damage in the low oxygen (hypoxic) cells found in tumors. Tirapazamine (TPZ) is the lead compound in this family. Here we report on the synthesis, crystal structure, and conformational analysis of a new analog, 3-cyclopropyl-1,2,4-benzotriazine 1,4-di-N-oxide (3). Compound 3 (C₁₀H₁₀N₃O₂) crystallized in the monoclinic space group C2/c. Unit cell parameters for 3: a = 16.6306 (12), b = 7.799 (5), c = 16.0113 (11) ?, α = 90, β = 119.0440 (10), γ = 90, and z = 8.