Structural Heterogeneity of Doubly-Charged Peptide b-Ions

Performing collisionally activated dissociation (CAD) and electron capture dissociation (ECD) in tandem has shown great promise in providing comprehensive sequence information that was otherwise unobtainable by using either fragmentation method alone or in duet. However, the general applicability of this MS³ approach in peptide sequencing may be undermined by the formation of non-direct sequence ions, as sometimes observed under CAD, particularly when multiple stages of CAD are involved. In this study, varied-sized doubly-charged b-ions from three tachykinin peptides were investigated by ECD. Sequence scrambling was observed in ECD of all b-ions from neurokinin A (HKTDSFVGLM-NH₂), suggesting the presence of N- and C-termini linked macro-cyclic conformers. On the contrary, none of the b-ions from eledoisin (pEPSKDAFIGLM-NH₂) produced non-direct sequence ions under ECD, as it does not contain a free N-terminal amino group. ECD of several b-ions from Substance P (RPKPQQFFGLM-NH₂) showed series of c_m-Lys fragment ions which suggested that the macro-cyclic structure may also be formed by connecting the C-terminal carbonyl group and the ε-amino group of the lysine side chain. Theoretical investigation of selected Substance P b-ions revealed several low energy conformers, including both linear oxazolones and macro-ring structures, in corroboration with the experimental observation. This study showed that a b-ion may exist as a mixture of several forms, with their propensities influenced by its N-terminus, length, and certain side-chain groups. Further, the presence of several macro-cyclic structures may result in erroneous sequence assignment when the combined CAD and ECD methods are used in peptide sequencing.     

Unusual Fragmentation of β-Linked Peptides by ExD Tandem Mass Spectrometry

Ion-electron reaction based fragmentation methods (ExD) in tandem mass spectrometry (MS), such as electron capture dissociation (ECD) and electron transfer dissociation (ETD) represent a powerful tool for biological analysis. ExD methods have been used to differentiate the presence of the isoaspartate (isoAsp) from the aspartate (Asp) in peptides and proteins. IsoAsp is a β₃-type amino acid that has an additional methylene group in the backbone, forming a C_α–C_β bond within the polypeptide chain. Cleavage of this bond provides specific fragments that allow differentiation of the isomers. The presence of a C_α–C_β bond within the backbone is unique to β-amino acids, suggesting a similar application of ExD toward the analysis of peptides containing other β-type amino acids. In the current study, ECD and ETD analysis of several β-amino acid containing peptides was performed. It was found that N–C_β and C_α–C_β bond cleavages were rare, providing few c and z type fragments, which was attributed to the instability of the C_β radical. Instead, the electron capture resulted primarily in the formation of a and y fragments, representing an alternative fragmentation pathway, likely initiated by the electron capture at a backbone amide nitrogen protonation site within the β amino acid residues.     

Kinetic discrimination in recognition of DNA quadruplex targets by guanine-rich heteroquadruplex-forming PNA probes

Guanine-rich peptide nucleic acid probes hybridize to DNA G quadruplex targets with high affinity, forming PNA-DNA heteroquadruplexes. We report a surprising degree of kinetic discrimination for PNA heteroquadruplex formation with a series of DNA targets. The fastest hybridization is observed for targets folded into parallel morphologies.     

Rainbows and glories in the angular scattering of the state-to-state F + H2 reaction at E(trans)=0.04088 eV

State-of-the-art differential cross sections (DCSs) have been reported by Wang et al. [Proc. Nat. Acad. Sci. (U.S.), 2008, 105, 6227] for the state-to-state F + H(2)→ FH + H reaction using fully quantum-state-selected crossed molecular beams. We theoretically analyze the angular scattering of this reaction, in order to quantitatively understand the physical content of structure in the DCSs. Three transitions are studied, v(i)=0, j(i)=0, m(i)=0 → v(f)=3, j(f)=0, 1, 2, m(f)=0 at a translational energy of 0.04088 eV, where v, j, m are the vibrational, rotational and helicity quantum numbers respectively for the initial and final states. The input to our analyses consists of accurate quantum scattering (S) matrix elements computed for the Fu-Xu-Zhang potential energy surface, as used by Wang et al. in a computational simulation of their experimental DCSs. We prove that the pronounced peak at forward angles observed in the experimental and simulated DCSs for all three transitions is a glory. At larger angles, it is demonstrated that the 000 → 300 and 000 → 310 DCSs both possess a broad farside rainbow, which is accompanied by diffraction oscillations. We confirm the conjecture of Wang et al. that these diffraction oscillations arise from nearside-farside (NF) interference. We find that the reaction is N dominant for all three transitions. The theoretical techniques used to analyze the angular scattering include uniform semiclassical theories of glory and of rainbow scattering. We also make the first application of a semiclassical formula that is uniform for both glory + rainbow scattering. In addition, structure in the DCSs is analyzed using NF theory and local angular momentum theory, in both cases with three resummations of the partial wave series for the scattering amplitude. We make the first explicit application of the Thiele rational interpolation formula to extract the position and residue of the leading Regge pole from a set of S matrix elements, thereby making contact with complex angular momentum theories of DCSs, which interpret the angular scattering in terms of Regge resonances. Our calculations complement the exit-valley vibrationally-adiabatic analysis of Wang et al.     

Semiclassical theory of molecular collisions: Real and complex-valued classical trajectories for collinear atom Morse oscillator collisions

Real and complex-valued classical trajectories have been calculated for the collinear collision of an atom with a Morse oscillator. They are used in three semiclassical approximations for the transition probability: a Bessel uniform approximation, an Airy uniform approximation and a primitive semiclassical approximation. Comparison with exact quantum results shows that the Bessel uniform approximation is accurate even for near elastic collisions where the Airy and primitive approximations break down. The Airy and Bessel approximations agree quite closely for inelastic collisions however. The primitive semiclassical approximation is less accurate than either the Airy or Bessel approximation.     

Evaluation of multidimensional canonical integrals in semiclassical collision theory

The evaluation of the multidimensional canonical integrals that occur in the uniform asymptotic representations of the S matrix in the semiclassical theory of inelastic and reactive molecular collisions is considered. For the non-separable two-dimensional canonical integral considered earlier, an exact series expansion is obtained with the help of convergence factors. This method avoids the complex variable techniques used previously. The uniform asymptotic formulae derived by Miller and Marcus are discussed, and compared with the approach adopted in the present paper.     

Theory of forward glory scattering for chemical reactions: New derivation of a uniform semiclassical formula for the scattering amplitude

The theory of forward glory scattering is investigated for a state-to-state chemical reaction whose scattering amplitude can be written as a Legendre partial wave series. Legendre series occur in the exact quantum theory of reactive scattering when the initial and final helicity quantum numbers are zero, as well as in many approximate theories of chemical reactions. The starting point for the semiclassical theory is a two-dimensional integral representation for the scattering amplitude. A uniform semiclassical approximation is derived that is valid for angles both on, and off, the axial caustic associated with the glory. The derivation is the first application to a concrete problem in molecular physics of a method outlined by J. N. L. Connor and H. R. Mayne in 1979 for the uniform semiclassical evaluation of multidimensional integrals. The approach exploits the theory of singularities of differential mappings. The key step in the derivation is an exact one-to-one change of variables in the neighbourhood of the stationary phase points that locally reduce the two-dimensional phase of the integrand to a non-polynomial canonical form. The derivation complements a different semiclassical glory analysis reported in a companion paper.     

Photoemission studies of pulsed-RF plasma nitrided ultra-thin SiON dielectric layers

Results are presented of a photoemission study of the electronic structure of SiON layers formed by a pulsed-RF decoupled plasma nitration (DPN) of ultra-thin SiO₂ grown base layers approximately 1.0 nm thick. The optical thickness of these device grade nitrided dielectric layers was in the range 1.4-1.6 nm. X-ray photoelectron spectroscopy (XPS) studies indicate that the nitrogen is incorporated in a single chemical environment at concentration levels in the range 15-17%. Angle resolved XPS measurements show that the nitrogen is distributed through the layer, with the binding energy of the N 1s peak at 398.3 eV which is indicative of a Si₃N₄-like chemical species in an oxide environment. High resolution core level photoemission studies of the spin orbit stripped Si 2p⁴⁺ peak revealed full width half maximum values in the range 1.4-1.55 eV, which are significantly larger than the 1.15 eV value reported for SiO₂ layers. Synchrotron radiation photoemission studies of the valence band spectra enable the valence band off-set at the Si/SON interface to be evaluated as 2.3 eV and to infer a conduction band off-set of 2.1 eV.     

Magnetic investigation of Er(C2O4) (C2O4)·3H2O

Single crystal susceptibilities of Er(C₂O₄) (C₂O₄H)·3H₂O are reported over the 1.5–20 K interval, and EPR spectra at 4.2 K of Y (C₂O₄) (C₂O₄H·3H₂O doped with Er³⁺ are also reported. The susceptibilities follow the CurieWeiss law, with g_| = 12.97 ± 0.05, g_⊥ = 2.98 ± 0.05, θ_| = ?0.25 ± 0.05 K, and θ_⊥ = ?0.12 ± 0.05 K.     

Ganglioside analysis by thin-layer chromatography matrix-assisted laser desorption/ionization orthogonal time-of-flight mass spectrometry

Metastable decomposition of ions generated in matrix-assisted laser desorption/ionization (MALDI) mass spectrometers complicates analysis of biological samples that have labile bonds. Recently, several academic laboratories and manufacturers of commercial instruments have designed instruments that introduce a cooling gas into the ion source during the MALDI event and have shown that the resulting vibrational cooling stabilizes these labile bonds. In this study, we compared stabilization and detection of desorbed gangliosides on a commercial orthogonal time-of-flight (oTOF) instrument with results we reported previously that had been obtained on a home-built Fourier transform mass spectrometer. Decoupling of the desorption/ionization from the detection steps resulted in an opportunity for desorbing thin-layer chromatography (TLC)-separated gangliosides directly from a TLC plate without compromising mass spectral accuracy and resolution of the ganglioside analysis, thus coupling TLC and oTOF mass spectrometry. The application of a declustering potential allowed control of the matrix cluster and matrix adduct formation, and, thus, enhanced the detection of the gangliosides.