Towards a full reference library of MS(n) spectra. Testing of a library containing 3126 MS2 spectra of 1743 compounds

A library consisting of 3766 MS(n) spectra of 1743 compounds, including 3126 MS2 spectra acquired mainly using ion trap (IT) and triple-quadrupole (QqQ) instruments, was composed of numerous collections/sources. Ionization techniques were mainly electrospray ionization and also atmospheric pressure chemical ionization and chemical ionization. The library was tested for the performance in identification of unknowns, and in this context this work is believed to be the largest of all known tests of product-ion mass spectral libraries. The MS2 spectra of the same compounds from different collections were in turn divided into spectra of 'unknown' and reference compounds. For each particular compound, library searches were performed resulting in selection by taking into account the best matches for each spectral collection/source. Within each collection/source, replicate MS2 spectra differed in the collision energy used. Overall, there were up to 950 search results giving the best match factors and their ranks in corresponding hit lists. In general, the correct answers were obtained as the 1st rank in up to 60% of the search results when retrieved with (on average) 2.2 'unknown' and 6.2 reference replicates per compound. With two or more replicates of both 'unknown' and reference spectra (the average numbers of replicates were 4.0 and 7.8, respectively), the fraction of correct answers in the 1st rank increased to 77%. This value is close to the performance of established electron ionization mass spectra libraries (up to 79%) found by other workers. The hypothesis that MS2 spectra better match reference spectra acquired using the same type of tandem mass spectrometer (IT or QqQ) was neither strongly proved nor rejected here. The present work shows that MS2 spectral libraries containing sufficiently numerous different entries for each compound are sufficiently efficient for identification of unknowns and suitable for use with different tandem mass spectrometers.     

The Influence of Sulfate‐Doping on the Nature of V Sites in VOx/TiO2 Catalysts

EPR, UV/Vis and FTIR spectroscopy as well as thermal analysis (TA/MS) were applied to study the influence of sulfate species present in the anatase support on the specific nature of VO_x species in supported VO_x/TiO₂ catalysts. Those sulfate species modify the local structure of the supported vanadyl species and lead to the formation of two types of VO²⁺ sites instead of only one type being formed on sulfate‐free anatase. EPR and FTIR spectroscopic measurements revealed that a part of the VO²⁺ species are directly bound to the surface sulfate species. By TA/MS it was found that SO₂ is released at lower temperature from VO_x/TiO₂ in comparison to the vanadium‐free support. The direct bonding between sulfate and VO_x species stabilizes the latter on the surface of VO_x/TiO₂ resulting in three effects: 1) a higher V site dispersion in comparison to sulfate‐free TiO₂, 2) a better resistance of surface vanadyls against diffusion into the bulk of the support and 3) a much faster reoxidation of reduced V sites than observed on sulfate‐free TiO₂.     

Evaluation of the contribution to hydration of nonelectrolytes from the hydrophobic effect

A new method was suggested for estimating the hydrophobic effect of contributions to the Gibbs energies and enthalpies of hydration of hydrocarbons, inorganic gases and rare gases. In accordance with this method the hydrophobic effect contribution to the Gibbs energy was evaluated from the difference between the hydration Gibbs energy of a solute and the non hydrophobic contribution. To estimate the latter value, the known dependence connecting the Gibbs energies of solvation of a solute in a number of aprotic solvents to the Hildebrand solubility parameter for these solvents was used. The non hydrophobic contribution to the Gibbs energy of hydration was calculated for various solutes from such dependences extended to water as solvent. The Hildebrand solubility parameter for water used in the calculation was corrected for the effect of association through hydrogen bonding. This correction was made by subtraction of the water self-association enthalpy from the enthalpy of vaporization of water. The evaluated Gibbs energies of the hydrophobic effect are positive for saturated hydrocarbons, inorganic gases and rare gases and linearly depend on the solute molecular refraction. The hydrophobic contribution to the hydration enthalpies of the solutes was calculated in the same manner as was made to calculate the hydrophobic contribution to Gibbs energies of hydration. Enthalpies of the hydrophobic effect for the solutes under study are negative.     

Stabilising small clusters: synthesis and characterisation of thermolabile [Gd4F7(15-crown-5)4][AsF6]5.6 SO2

Addition of 15-crown-5 to [GdF(AsF6)2], both dissolved in liquid SO2, and crystallisation at -30 degrees C has led to the isolation of the tetranuclear ionic complex [Gd4F7(15-crown-5)4][AsF6]5.6 SO2 which is stable up to--10 degrees C where SO2 loss leads to loss of crystallinity.     

Computational study of the aminolysis of esters. The reaction of methylformate with ammonia

The aminolysis of esters is a basic organic reaction considered as a model for the interaction of carbonyl group with nucleophiles. In the present computational study the different possible mechanistic pathways of the reaction are reinvestigated by applying higher level electronic structure theory, examining the general base catalysis by the nucleophile, and a more comprehensive study the solvent effect. Both the ab initio QCISD/6-31(d,p) method and density functional theory at the B3LYP/6-31G(d) level were employed to calculate the reaction pathways for the simplest model aminolysis reaction between methylformate and ammonia. Solvent effects were assessed by the PCM method. The results show that in the case of noncatalyzed aminolysis the addition/elimination stepwise mechanism involving two transition states and the concerted mechanism have very similar activation energies. However, in the case of catalyzed aminolysis by a second ammonia molecule the stepwise mechanism has a distinctly lower activation energy. All transition states in the catalyzed aminolysis are 10-17 kcal/mol lower than those for the uncatalyzed process.     

Analysis of post-translational modification and characterization of the domain structure of dynamin A from Dictyostelium discoideum

The post-translational modifications of the 96 kDa protein dynamin A from Dictyostelium discoideum were analyzed using Q-TOF mass spectrometry. The accurate molecular mass of the intact protein revealed a covalent modification causing an additional mass of 42 Da. The modification could be identified as N-terminal acetylation by tandem mass spectrometry. Extracted ion chromatograms for the a(1) and b(1) ion of the tryptic T1 peptide were used to detect the acetylated peptide within 54 nanoelectrospray ionization tandem mass spectra. Owing to the accurate molecular mass of the intact protein, additional covalent modifications could be excluded. In addition to the covalent modification, the domain structure of dynamin A was determined by applying a combination of limited proteolysis, sodium dodecylsulfate polyacrylamide gel electrophoresis, automated tandem mass spectrometry and protein database searching.     

E-1,2-Dichlorovinyl ethers as irreversible protease inhibitors

The synthesis of a novel motif for threonine protease inhibition is described. The desired E-1,2-dichlorovinyl ethers are obtained from alcohols and trichloroethylene as single diastereomers. Aqueous treatment at pH 11 unmasks the hidden α-chloroacetate, which is required for the reaction with the active site of the protease.     

A general method for preparation of metal carbenes via solution- and polymer-based approaches

A new general, synthetically simple, and safe method for the preparation of metal carbene complexes, which is based on diphenyl sulfonium salts as carbenoid precursors, has been developed, and its scope and applications were studied. In general, deprotonation of a sulfonium salt with a base results in a sulfur ylide, which, in turn, reacts with an appropriate metal precursor to give the corresponding metal carbene complex. Thus, starting from benzyldiphenylsulfonium salt, the complexes (PCX)Rh=CHPh (X = P, N) were prepared in quantitative yield. Syntheses of Grubbs' catalyst, (PCy(3))(2)Cl(2)Ru=CHPh, and of Werner's carbene, [Os(=CHPh)HCl(CO)(P(i)Pr(3))(2)], were achieved by this method. Novel trans-bisphosphine Rh and Ir carbenes, ((i)Pr(3)P)(2)(Cl)M=CHPh, which could not be prepared by other known methods, were synthesized by the sulfur ylide approach. The method is not limited to metal benzylidenes, as demonstrated by the preparation of the Ru vinyl-alkylidene, (PCy(3))(2)Cl(2)Ru=CH-CH=CH(2), methoxycarbonyl-alkylidene, (PCy(3))(2)Cl(2)Ru=CH(CO(2)Me), and alkylidene (PCy(3))(2)Cl(2)Ru=CH(CH(3)), (PCy(3))(2)Cl(2)Ru=CH(2) compounds. The problem of recycling of starting materials as well as the issue of facile purification of the product metal carbene complex were addressed by the synthesis of a polymer-supported diarylsulfide, the carrier of the carbenoid unit in the process. Based on the sulfur ylide route, a methodology for the synthesis of metallocarbenes anchored to a polymer via the carbene ligand, using a commercial Merrifield resin, was developed.     

Spin–orbit coupling in oxygen containing diradicals

Intermediate diradicals which occur in the Paterno–Büchi photocycloaddition and in the Norrish type I photoreactions have been calculated taking into account the spin–orbit coupling (SOC) between the singlet (S) and triplet (T) states. Reaction paths for the photocycloaddition of formaldehyde to ethene and the diradical products of the α-cleavage of cyclohexanone have been optimized by the MNDO CI method for a number of different singlet and triplet states. SOC integrals are calculated by an effective one-electron approximation. Intermediate diradicals in the Paterno–Büchi reaction and the SOC effects are also studied ab initio with CAS SCF geometry optimization in a TZV basis set. Both methods predict a large SOC matrix element between the S and T states in the course of the C–C attack, while the SOC integral is two orders of magnitude smaller for the diradical produced in the C–O attack. In the Norrish type I photoreaction the oxygen atom also produces some nonzero contribution to the SOC integral which governs intersystem crossing in a ·C–C· diradical. For the diradicals produced by the α-cleavage of cyclohexanone a vibronic interaction is responsible for the SOC mixing between the lowest S and T states. The importance of one-center versus two-center SOC contributions in diradicals is briefly discussed.     

Final elucidation of the absolute configuration of the signal metabolite hormaomycin

The complete absolute configuration of hormaomycin 1 a has been established by HPLC and HPLC/MS experiments with appropriately derivatized 4-propylprolines, (2S,4S)-6 and (2R,4R)-6, as well as 4-(Z)-propenylprolines, cis-5 and trans-5, and also feeding experiments with enantiomerically pure samples of the deuterium-labeled 3-(2'-nitrocyclopropyl)alanine, (2S)-3,3-[D2]15 and (2S)-2,2'-[D2]15, and 4-(Z)-propenylproline 2',4-[D2]-(2S,4R)-5. The latter five amino acids were prepared for the first time and allowed one to unequivocally assign the hitherto unknown absolute configurations of the last four stereocenters in hormaomycin 1 a. As a bonus, some new information about the biosynthesis of this molecule has also been gathered.