High-sensitivity analysis of specific peptides in complex samples by selected MS/MS ion monitoring and linear ion trap mass spectrometry: application to biological studies

Mass spectrometry (MS) is a technique of paramount importance in Proteomics, and developments in this field have been possible owing to novel MS instrumentation, experimental strategies, and bioinformatics tools. Today it is possible to identify and determine relative expression levels of thousands of proteins in a biological system by MS analysis of peptides produced by proteolytic digestion. In some situations, however, the precise characterization of a particular peptide species in a very complex peptide mixture is needed. While single-fragment ion-based scanning modes such as selected ion reaction monitoring (SIRM) or consecutive reaction monitoring (CRM) may be highly sensitive, they do not produce MS/MS information and their actual specificity must be determined in advance, a prerequisite that is not usually met in a basic research context. In such cases, the MS detector may be programmed to perform continuous MS/MS spectra on the peptide ion of interest in order to obtain structural information. This selected MS/MS ion monitoring (SMIM) mode has a number of advantages that are fully exploited by MS detectors that, like the linear ion trap, are characterized by high scanning speeds. In this work, we show some applications of this technique in the context of biological studies. These results were obtained by selecting an appropriate combination of scans according to the purpose of each one of these research scenarios. They include highly specific identification of proteins present in low amounts, characterization and relative quantification of post-translational modifications such as phosphorylation and S-nitrosylation and species-specific peptide identification.     

New selective haloform-type reaction yielding 3-hydroxy-2,2-difluoroacids: theoretical study of the mechanism

Experimental results of an unprecedented haloform-type reaction in which 4-alkyl-4-hydroxy-3,3-difluoromethyl trifluoromethyl ketones undergo base-promoted selective cleavage of the CO-CF(3) bond, yielding 3-hydroxy-2,2-difluoroacids and fluoroform, are rationalized using DFT (B3LYP) calculations. The gas-phase addition of hydroxide ion to 1,1,1,3,3-pentafluoro-4-hydroxypentan-2-one (R) is found to be a barrierless process, yielding a tetrahedral intermediate (INT), involving a DeltaG(r)(298 K) of -61.4 kcal/mol. The CO-CF(3) bond cleavage in INT leads to a hydrogen-bonded [CH(3)CHOHCF(2)CO(2)H...CF(3)](-) complex by passage through a transition structure (TS1) with a DeltaG()(298 K) of 20.8 kcal/mol and a DeltaG(r)(298 K) of 9.8 kcal/mol. This complex undergoes a proton transfer between its components, yielding a hydrogen-bonded [CH(3)CHOHCF(2)CO(2)...CHF(3)](-) complex. This process has associated with it a DeltaG()(298 K) of only 3.1 kcal/mol and a DeltaG(r)(298 K) of -43.3 kcal/mol. The CO-CF(2) bond cleavage in INT leads to a hydrogen-bonded [CH(3)CHOHCF(2)...CF(3)CO(2)H](-) complex by passage through a transition structure (TS3) with a DeltaG()(298 K) of 29.2 kcal/mol and a DeltaG(r)(298 K) of 25.1 kcal/mol. The lower energy barrier found for CO-CF(3) bond cleavage in INT is ascribed to the larger number of fluorine atoms stabilizing the negative charge accumulated on the CF(3) moiety of TS1, as compared to the number of fluorine atoms stabilizing the negative charge on the CH(3)CHOHCF(2) moiety of TS3. The solvent-induced effects on the two pathways, introduced within the SCRF formalism through PCM calculations, do not reverse the predicted preference of the CO-CF(3) over the CO-CF(2) bond cleavage of R in the gas phase.     

Organic-inorganic hybrids based on novel bimolecular [Si2W22Cu2O78(H2O)]12- polyoxometalates and the polynuclear complex cations [Cu(ac)(phen)(H2O)]n n+ (n=2, 3)

The reaction of a monosubstituted Keggin polyoxometalate (POM) generated in situ with copper-phenanthroline complexes in excess ammonium or rubidium acetate led to the formation of the hybrid metal organic-inorganic compounds A7[Cu2(ac)2(phen)2(H2O)2][Cu3(ac)3(phen)3(H2O)3][Si2W22Cu2O78(H2O)].approximately 18 H2O (A=NH4+ (1), Rb+ (2); ac=acetate; phen=1,10-phenanthroline). These compounds are constructed from inorganic and metalorganic interpenetrated sublattices containing the novel bimolecular Keggin POM, [Si2W22Cu2O78(H2O)]12-, and Cu-ac-phen complexes, [Cu(ac)(phen)(H2O)]n n+ (n=2, 3). The packing of compound 1 can be viewed as a stacking of open-framework layers parallel to the xy plane built of hydrogen-bonded POMs, and zigzag columns of pi-stacked Cu-ac-phen complex cations running along the [111] direction. Magnetic and EPR results are discussed with respect to the crystal structure of the compounds. DFT calculations on [Cu(ac)(phen)(H2O)]n n+ cationic complexes have been performed, to check the influence of packing in the complex geometry and determine the magnetic exchange pathways.     

Structure and Conformation of Photosynthetic Pigments and Related Compounds. 12. A Crystallographic Analysis of Porphyrin-quinones and Their Precursors

Abstract. A comprehensive crystallographic analysis of 10 porphyrin quinone precursors (dimethoxybenzene derivatives), and six porphyrin quinones has been performed. The free bases and zinc(II) complexes of the porphyrin quinones are of the 5,10,15-triaryl/alkyl-20-quinone-porphyrin type and carry various bridging and quinone units. The structural and conformational parameters were determined for all compounds; the donor-acceptor separation distances range from 6.3 to 10.9 Å. Knowledge of these data is a prerequisite for a detailed interpretation of theoretical and spectroscopic studies on such systems. Despite the obvious influence of the type and geometry of the bridging unit and quinone on the spatial arrangement of the donor and acceptor components, a large variety of different packing arrangements in the crystal were observed. These include π stacking, aggregate formation and axial ligation in the zinc(II) porphyrins. The latter often utilized the quinone (or dimethoxy) oxygen atoms for coordination to zinc(II) centers leading to porphyrin quinone dimers and even polymers.     

Modeling and experiment reveal an unexpected stereoelectronic effect on conformation and scalar couplings of alpha-aminoorganostannanes, with possible relevance to the tin-lithium exchange reaction

The solution conformation of N-methyl-2-(tributylstannyl)piperidines has been determined through the use of vicinal 119Sn-13C coupling constants, revealing a conformational distortion caused by an unexpected stereoelectronic effect in some cases. Specifically, the "equatorial" conformer is distorted into a half-chair, in which the nitrogen lone pair eclipses the C-Sn bond. This distortion, which "costs" approximately 1 kcal/mol, correlates with a conformational dependence of geminal 119Sn-15N couplings and a possible correlation with reactivity in the tin-lithium exchange reaction.     

Edge effects, electronic arrangement, and aromaticity patterns on finite-length carbon nanotubes

Previous investigations have revealed that even long carbon nanotubes (CNTs) retain bond patterns that are characterized by the localization of Clar rings. Even for CNTs with 10 nm length, an alternated, oscillating structure of Clar and Kekulé patterning was also found, indicating that these arrangements may possibly persist for even longer nanotubes, given that they are finite. In the present work, we perform a detailed and comprehensive theoretical study of this phenomenon, in order to find the causes that give rise to these patterns. A complete set of CNTs with different chiralities, diameters (up to 2 nm), lengths (up to 10 nm) and endings (capped, uncapped, and tailored endings) was considered for such purposes. The results indicate that the Clar patterning appears not only on armchair CNTs, but also on those with chiral angle values close to 30°, and this results in a stabilization of the structure, when compared with the uniform, zigzag CNTs. This stabilizing effect points to the causes that underlie the three Nakamura CNT types, resulting as the superposition of structures with a maximal number of Clar rings. Although there is a strict dependence on the border shape, the main cause of the bond patterning in long tubes is to be found in the intrinsic wrapping of each CNT, because the type and number of oscillations present in the longest structures do not depend on the particular length. Nevertheless, the three Nakamura types of armchair tubes appear to subsist beyond the appearance of oscillations, because each of these sets evolves in a different manner, and energy properties that link them together. Apart from the geometry, Clar patterning was investigated through NICS (Nucleus Independent Chemical Shifts) measures, which reveal a connection between the Clar rings and a local concentration of aromaticity.     

Self-recognition and hydrogen bonding by polycyclic bridgehead monoalcohols

Our interest in the relationship between the hydrogen bonding motifs displayed by monoalcohols and the properties of the solids which contain these motifs has led us to determine the crystal structures of three polycyclic bridgehead monoalcohols. One C10H16O isomer crystallises in the space group P2(1)2(1)2(1) but the three molecules which comprise the asymmetric unit are related approximately by the operations of a 3(1) screw axis. They are linked by hydrogen bonds to form an infinite helix. A second C10H16O isomer forms rings containing four molecules joined by cooperative hydrogen bonds. The chiral space group P4(1)2(1)2 accommodates molecules of the S,S and R,R enantiomers in the molar ratio 92:8 (ee 84%) owing to disorder. A related C9H14O2 keto-alcohol forms infinite chains by C-OH...O = C hydrogen bonding. These hydrogen bond motifs are shown to be typical for 45 tertiary monoalcohols, CmHnOH, present in the Cambridge Structural Database. Tertiary monoalcohols display in a more pronounced form the strong preferences for trigonal and tetragonal space groups and for asymmetric units containing several molecules which are established features of the crystallochemistry of monoalcohols.     

Room-temperature synthesis and crystal,magnetic, and electronic structure of the first silver copper oxide

Ag(2)Cu(2)O(3) is the first known silver copper oxide. It was prepared by coprecipitation at room temperature and ambient pressure and shows an increased thermal stability compared with silver oxides. The crystal structure (tetragonal, a = 5.8862(2) A, c = 10.6892(4) A, Z = 4, I4(1)/amd) was refined from neutron and X-ray powder diffraction data, and it is related to that of the mineral paramelaconite (Cu(4)O(3)). In addition to a thorough characterization (chemical and TG analyses, XPS, crystal structure, and electrochemical, magnetic, and transport properties), we have carried out band structure calculations [extended Hückel tight binding (EHTB) and spin polarized density functional (DFT) band calculations] for the title silver copper oxide and for the related paramelaconite structure (Cu(II)-Cu(I) mixed-valence system) with special incidence into the magnetic behavior and coupling constants in these magnetically novel 3-D compounds. This new oxide represents an important precedent in solid state inorganic chemistry but also has potential interest concerning its magnetic, electrochemical, and catalytic properties.     

A method for determining electrophoretic and electroosmotic mobilities using AC and DC electric field particle displacements

We have developed a method for measuring the electrophoretic mobility of submicrometer, fluorescently labeled particles and the electroosmotic mobility of a microchannel. We derive explicit expressions for the unknown electrophoretic and the electroosmotic mobilities as a function of particle displacements resulting from alternating current (AC) and direct current (DC) applied electric fields. Images of particle displacements are captured using an epifluorescent microscope and a CCD camera. A custom image-processing code was developed to determine image streak lengths associated with AC measurements, and a custom particle tracking velocimetry (PTV) code was devised to determine DC particle displacements. Statistical analysis was applied to relate mobility estimates to measured particle displacement distributions.     

Diastereoselective reactions in glycine templates containing an ent-ardeemin fragment

Self-consistent reaction field solvation models derived from SCF-MO calculations are shown to be reliable in modeling the diastereoselectivity of the reactions of the anion and cation derived from (4S)-2,4-dimethyl-2,4-dihydro-1H-pyrazino[2,1-b]quinazoline-3,6-dione (1) at C(1) with electrophiles and nucleophiles, respectively. The found anti/syn ratio of compound 8, which is a seco-ent-ardeemin analogue obtained by alkylation of 1 with gramine methiodide, confirms this computational model. A close similarity between the calculated geometry of the piperazine ring in the anti isomers of 1,2,4-trialkyl derivatives and that deduced from their (1)H NMR (solution) and X-ray data has been also established.