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.     

Induced-fit recognition by p-carboxylatocalix[4]arene hosts

Calix[4]arene derivatives bearing anionic carboxylato groups at the upper rim (p-carboxylatocalix[4]arenes) are able to ‘grab’ paraquat dicationic guest through an induced-fit mechanism, which originates from the conformational mobility of calixarene skeleton.     

Two 1-substituted 4-nitro­imidazoles

Crystalline 4-nitro-1-phenyl­imidazole, C₉H₇N₃O₂, (I), and 4′-­nitro-1-phenyl-4,1′-bii­imidazole, C₁₂H₉N₅O₂, (II), contain C—H⃛O and C—H⃛N hydrogen bonds, connecting the mol­ecules into infinite chains. The aromatic fragments in both compounds are nearly planar. The dihedral angles between the benzene and imidazole rings are 26.78 (5)° in (I) and 29.36 (8)° in (II).     

Determination of trace amounts of cobalt in water by solid-phase spectrophotometry after preconcentration on a nitroso R salt chelating resin

A sensitive method for the determination of microamounts of cobalt by ion-exchanger spectrophotometry has been developed. The chromogenic agent, Nitroso-R-Salt (NRS), was loaded on an anionic-exchange resin (Amberlite CG-400). The absorbance of the NRS-cobalt complex on the chelating resin was measured at 508 nm. The best conditions for the preconcentration of cobalt on the resin before the spectrophotometric determination were a pH value of 6, temperature of 80 °C, and heating times of 45 or 90 min for 50 and 400 ml of sample, respectively. The detection limits were 27 ng/ml (50-ml samples) and 1.8 ng/ml (400-ml samples). Interference by other metals was investigated. The method is useful for determination of cobalt in natural waters.     

Thermodynamics of alcohols and monosaccharides in aqueous solutions of thiourea at 25°C

The excess enthalpies of twelve ternary aqueous solutions of alcohols or monosaccharides containing thiourea have been determined by flow microcalorimetry at 25°C. The coefficients of the virial expansion of the excess enthalpies are compared with those reported in the literature for the same ternary solutions containing urea in place of thiourea. The cross-interaction coefficients are positive for the thiourea-alcohol systems and depend on the length and branching of the alkyl chain of the alcohols. On the other hand, they are negative for the thiourea-monosaccharide systems. Thus, thiourea, as urea, can be used as a probe to reveal differences in the behavior of families of solutes characterized by the same functional groups. The results can be interpreted in terms of the relative stabilities of hydration cospheres of hydrophobic or hydrophilic solutes toward a chaotropic agent such as thiourea.Presented at the sixth Italian meeting on Calorimetry and Thermal Analysis (AICAT) held in Naples, December 4–7, 1984.     

Nanotubes Made from Deeply Undercooled Cryolite/Alumina Melts

The rapid‐solidification processing (by a cooling rate of 10⁵–10⁶ K/s) was used for the preparation of deeply undercooled cryolite/alumina (Na₃AlF₆/Al₂O₃) melts. We found a mass of nanotubes on the surface of these undercooled melts. The nanotubes were preferentially located on the defect places of the surface with the following approximate dimensions: base≈100×100 nm, length≈1000 nm. The solidified samples with the nanotubes on the surface were analyzed by scanning electron microscopy (SEM), energy‐dispersive X‐ray spectroscopy (EDX), X‐ray diffraction (XRD), and infrared spectroscopy (IR).     

New Schiff base complexes of ruthenium(III) and their use as catalysts for O-allyl systems isomerization

Seven new ruthenium(III) complexes of the general formula [RuCl(PPh₃)LL′] · xH₂O (LL′ = [ONNO] = symmetrical and unsymmetrical Schiff base derivatives of trans-1,2-diaminocyclohexane and 2-hydroxynaphthaldehyde as well as R-salicylaldehydes, x = 0–3) have been synthesized. The complexes were characterized by physico-chemical and spectroscopic techniques. The catalytic activities of the complexes in the isomerization reaction of selected O-allyl systems, i.e., 1,4-diallyloxybutane and 4-allyloxybutan-1-ol have been studied. Some of the complexes showed high efficiency and E-stereoselectivity in double bond migration of allyl group to 1-propenyl group and high selectivity of isomerization of allyloxyalcohol to cyclic acetal.     

Crystalline structure of sequential poly(ester amide)s derived from glycolic acid, 1,6‐hexanediamine,and even aliphatic dicarboxylic acids

Basic structural data of two sequential poly(ester amide)s derived from glycolic acid, 1,6‐hexanediamine, and adipic acid or dodecanodioic acid have been determined by means of X‐ray and electron diffraction patterns from fibers and single crystals. Chain‐folded lamellar crystals were obtained by isothermal crystallization from diol or glycerine solutions, and the crystalline habit was investigated by real space electron microscopy. Polyethylene decoration techniques were applied to evaluate the regularity of the folding surfaces. Spherulites prepared from evaporation of formic acid solutions were also studied. The two sequential poly(ester amide)s crystallized according to triclinic and monoclinic unit cells, in which the a crystallographic parameter was close to the typical distance between hydrogen‐bonded chains. Projections viewed down the chain axis revealed differences in the packing mode since oblique and rectangular cells were found for the adipic acid and dodecanodioic acid derivatives, respectively. Both structures can be envisaged as a stacking of hydrogen‐bonded sheets although clear differences concerning the shift between consecutive sheets and the number of layers comprising the unit cell were found. The large unit cells that have been deduced seem to be a consequence of the different packing preferences of the diester and diamide moieties. Both polymers have a molecular conformation that deviates from the all‐trans conformation typical of aliphatic polyamides and polyesters with a large number of methylene groups. © 2008 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 47: 194–206, 2009