Fragmentation of N-linked glycans with a matrix-assisted laser desorption/ionization ion trap time-of-flight mass spectrometer

N-Linked glycans were ionized from several matrices with a Shimadzu-Biotech AXIMA-QIT matrix-assisted laser desorption/ionization quadrupole ion trap time-of-flight mass spectrometer. [M+Na]+ ions were produced from all matrices and were accompanied by varying amounts of in-source fragmentation products. The least fragmentation was produced by 2,5-dihydroxybenzoic acid and the most by alpha-cyano-4-hydroxycinnamic acid and 6-aza-2-thiothymine. Sialic acid loss was extensive but could be prevented by formation of methyl esters. Fragmentation produced typical low-energy-type spectra dominated by ions formed by glycosidic cleavages. MS(n) spectra (n = 3 and 4) were used to probe the pathways leading to the major diagnostic ions. Thus, for example, an ion that was formed by loss of the core GlcNAc residues and the 3-antenna was confirmed as being formed by a B/Y rather than a C/Z mechanism. The proposed structures of several cross-ring cleavage ions were confirmed and it was shown that MS3 spectra could be obtained from as little as 10 fmol of glycan.     

Synthesis of 17β-hydroxy-1′-H-5α-androst-2-eno[3,2-b]pyrrole and 17β-hydroxy-1′-H-5α-androst-3-eno[3,4-b]pyrrole from O-(2-hydroxyethyl)ketoxime precursors

Pyrrolosteroids such as 17β-hydroxy-1′-H-5α-androst-2-eno[3,2-b]pyrrole ( 1 ) and the novel 17β-hydroxy-1′-H-5α-androst-3-eno[3,4-b]pyrrole ( 12 ) can be synthesized from the corresponding O-(2-hydroxyethyl)ketoxime precursors. In the case of 1 , yields compare favourably with previously reported literature methods.     

Secondary and Tertiary Structure of Polysaccharides in Solutions and Gels

Many polysaccharide chains can adopt ordered helical and ribbon-like secondary structures. It seems however that these chains are often so stiff and extended that the cooperative interactions necessary for stability in the solvent environment can only be achieved when inter-chain as well as intra-chain interactions are favorable. Hence we commonly find two-or more-stranded associations of helices, of ribbons, or of helices with ribbons. These can be regarded as tertiary and higher levels of structure. The ordered secondary structure characteristically requires a regular repeating sequence of sugar residues, and the termination of this sequence by insertion of a residue of different type may also terminate the secondary structure and hence the association in which it is involved. This is the mechanism by which native polysaccharides may link up to form three dimensional networks, or gels, in which state they perform their natural roles in maintaining the hydration and integrity of biological tissues. For several polysaccharides there is evidence that the mechanism of biological control over the fine topology and properties of the gel network is mediated by enzymes which modify sugar residues at the polymer level to change the pattern of “interrupting” sugar residues.     

A critical comparison of approximation methods and models for equilibrium properties of low-barrier hydrogen bonds

Recent experimental evidence has led to the conclusion that short, strong hydrogen bonds can stabilize transition states of enzyme catalyzed biochemical reactions. Evidence for such hydrogen bonds is the low value of the isotopic fractionation factor, phi, which is defined as the equilibrium constant for the generic reaction, R-H + DOH <--> R-D + HOH, where H is the hydrogen atom participating in the low-barrier hydrogen bond in a molecule R-H. In this work we assess two approximation methods for computing the isotopic fractionation factors for single and multidimensional systems containing a low-barrier hydrogen bond. These methods are WKB and an approach that corrects the classical partition function via a quantum correction factor. We find that the latter approach is universally accurate and applicable in both single and multidimensional systems containing a low-barrier hydrogen bond. We also assess two different models for the coupling of a molecule's low-barrier hydrogen bond to other degrees of freedom, both internal and external to the molecule, and show that each leads to a lowering of the fractionation factor.     

Overtone spectroscopy of H2O clusters in the V(OH) = 2 manifold: infrared-ultraviolet vibrationally mediated dissociation studies

Spectroscopy and predissociation dynamics of (H2O)2 and Ar-H2O are investigated with vibrationally mediated dissociation (VMD) techniques, wherein upsilon(OH) = 2 overtones of the complexes are selectively prepared with direct infrared pumping, followed by 193 nm photolysis of the excited H2O molecules. As a function of relative laser timing, the photolysis breaks H2O into OH and H fragments either (i) directly inside the complex or (ii) after the complex undergoes vibrational predissociation, with the nascent quantum state distribution of the OH photofragment probed via laser-induced fluorescence. This capability provides the first rotationally resolved spectroscopic analysis of (H2O)2 in the first overtone region and vibrational predissociation dynamics of water dimer and Ar-water clusters. The sensitivity of the VMD approach permits several upsilon(OH) = 2 overtone bands to be observed, the spectroscopic assignment of which is discussed in the context of recent anharmonic theoretical calculations.     

Lysine peroxycarbamates: free radical-promoted peptide cleavage

Strategies are reported that combine in one step a predictable chemical-based protein digestion with mass spectrometry. Lysine residue amino groups in peptides and proteins are modified by reaction with a peroxycarbonate derived from p-nitrophenol, and tert-butyl hydroperoxide. The peroxycarbonate reacts with lysine residues in peptides and proteins, and the resulting lysine peroxycarbamates undergo homolytic fragmentation under conditions of low-energy collision-induced dissociation (CID). Observed fragmentation of the peptides involves apparent free radical processes including Hofmann-L?ffler-type rearrangements that lead to peptide chain fragmentation. Strategies for directed cleavage of peptides by free radical promoted processes are feasible, and such strategies may well simplify schemes for protein analysis.     

SINGLE-STRAND BREAKS IN THE DNA OF THE uvrA AND uvrB STRAINS OF ESCHERICHIA COLI K-12 AFTER ULTRAVIOLET IRRADIATION

Abstract— DNA single-strand breaks were produced in uvrA and uvrB strains of E. coli K-12 after UV (254 nm) irradiation. These breaks appear to be produced both directly by photochemical events, and by a temperature-dependent process. Cyclobutane-type pyrimidine dimers are probably not the photoproducts that lead to the temperature-dependent breaks, since photoreactivation had no detectable effect on the final yield of breaks. The DNA strand breaks appear to be repairable by a process that requires DNA polymerase I and polynucleotide ligase, but not the recA, recB, recF, lexA 101 or uvrD gene products. We hypothesize that these temperature-dependent breaks occur either as a result of breakdown of a thermolabile photoproduct, or as the initial endonucleolytic event of a uvrA , uvrB -independent excision repair process that acts on a UV photoproduct other than the cyclobutane-type pyrimidine dimer.     

Molecular orbital energy levels for the sulfate Ion

A series of semiempirical molecular orbital calculations for the SO₄ ^2? ion is described. These calculations show the effect on the order of the molecular orbital energy levels of a) using the Wolfsberg-Helmholz approximation, b) using the Cusachs approximation, c) variation of the proportionality constant, F, in the Wolfsberg-Helmholz approximation, d) inclusion of d-orbitals in the basis set, and e) variation of ζ_d when d-orbitals are included. It is found that the highest filled level is t ₁ for all the Wolfsberg-Helmholz calculations when d-orbitals are included and is 3t ₂ for all the other calculations.     

Absorption,fluorescence and phosphorescence spectra of the singlet and triplet states of s-tetrazine in the crystal and in mixed crystals at low temperatures

The electronic absorption, fluorescence and phosphorescence spectra of s-tetrazine at low temperatures (4.2-1.5 K) are reported and analyzed in the neat crystal and in several mixed crystals. The ³B_3u-¹A_g (nπ^*) origin is at 18414 ± 5 cm^?1 for neat tetrazine. In the mixed crystal several sites identified. The lowest energy origin is at 17453 cm^?1 for tetrazine in pyrazine; 17 701 cm^?1 in pyrimidine; and 17 676 cm^?1 in pyridazine. The ^eB_3u-¹A_g (nπ^*) origin is at 14 096 ± 2 cm^?1 for the neat crystal. The phosphorescence lifetime of neat tetrazine is measured to be 96.8 ± 2.1 μs at 4.2 and 1.8 K. All the spectra are predominately composed of members of progressions in a single totally symmetric mode (ν_6a) built upon site origins and vibrational fundamentals. The ν_6a interval is: 743 (¹A_g), 715 (³B_3u), and 709 cm^?1 (¹B_3u) in the neat tetrazine crystal; 732 (¹A_g) and 705 cm^?1 (¹B_3u in pyrazine host, 737 (¹A_g) and 701 cm^?1 (¹B_3u) in pyrimidine host, and 732 (¹A_g) and 703 cm^?1 (¹B_3u) in pyridazine host mixed crystals. All emission spectra may be analyzed by Oi → (ν″_6a)^o_n (i), i indicating the observed s     

Uniqueness of barbilian domains

W. Leissner has developed a plane geometry over any Z-ring R, in which a point is an element of R×R and a line is a set of the form {(x+ ra, y + rb):r R} where (x,y) R×R and (a,b) is from a Barbilian domain, i.e., a set of unimodular pairs from R×R satisfying certain axioms. In this note we generalize results of W. Benz guaranteeing the uniqueness of Barbilian domains over several classes of commutative rings. The author wishes to thank Gordon Keller and Douglas Costa for fruitful discussions, the referee for his improvements, and the University of Virginia for its hospitality while this work was done.