Charge remote fragmentation in electron capture and electron transfer dissociation

Secondary fragmentations of three synthetic peptides (human αA crystallin peptide 1-11, the deamidated form of human βB2 crystallin peptide 4-14, and amyloid β peptide 25-35) were studied in both electron capture dissociation (ECD) and electron-transfer dissociation (ETD) mode. In ECD, in addition to c and z· ion formations, charge remote fragmentations (CRF) of z· ions were abundant, resulting in internal fragment formation or partial/entire side-chain losses from amino acids, sometimes several residues away from the backbone cleavage site, and to some extent multiple side-chain losses. The internal fragments were observed in peptides with basic residues located in the middle of the sequences, which was different from most tryptic peptides with basic residues located at the C-terminus. These secondary cleavages were initiated by hydrogen abstraction at the α-, β-, or γ-position of the amino acid side chain. In comparison, ETD generates fewer CRF fragments than ECD. This secondary cleavage study will facilitate ECD/ETD spectra interpretation, and help de novo sequencing and database searching.     

Semiclassical glory analyses in the time domain for the H + D2(v(i) = 0, j(i) = 0) → HD(v(f) = 3, j(f) = 0) + D reaction

We make the first application of semiclassical (SC) techniques to the plane-wavepacket formulation of time-domain (T-domain) scattering. The angular scattering of the state-to-state reaction, H + D(2)(v(i) = 0, j(i) = 0) → HD(v(f) = 3, j(f) = 0) + D, is analysed, where v and j are vibrational and rotational quantum numbers, respectively. It is proved that the forward-angle scattering in the T-domain, which arises from a delayed mechanism, is an example of a glory. The SC techniques used in the T-domain are: An integral transitional approximation, a semiclassical transitional approximation, a uniform semiclassical approximation (USA), a primitive semiclassical approximation and a classical semiclassical approximation. Nearside-farside (NF) scattering theory is also employed, both partial wave and SC, since a NF analysis provides valuable insights into oscillatory structures present in the full scattering pattern. In addition, we incorporate techniques into the SC theory called "one linear fit" and "two linear fits", which allow the derivative of the quantum deflection function, Θ?(')(J), to be estimated when Θ?J exhibits undulations as a function of J, the total angular momentum variable. The input to our SC analyses is numerical scattering (S) matrix data, calculated from accurate quantum collisional calculations for the Boothroyd-Keogh-Martin-Peterson potential energy surface No. 2, in the energy domain (E-domain), from which accurate S matrix elements in the T-domain are generated. In the E-domain, we introduce a new technique, called "T-to-E domain SC analysis." It half-Fourier transforms the E-domain accurate quantum scattering amplitude to the T-domain, where we carry out a SC analysis; this is followed by an inverse half-Fourier transform of the T-domain SC scattering amplitude back to the E-domain. We demonstrate that T-to-E USA differential cross sections (DCSs) agree well with exact quantum DCSs at forward angles, for energies where a direct USA analysis in the E-domain fails.     

Transient responses of a wetting film to mechanical and electrical perturbations

This article reports real-time observations and detailed modeling of the transient response of thin aqueous films bounded by a deformable surface to external mechanical and electrical perturbations. Such films, tens to hundreds of nanometers thick, are confined between a molecularly smooth mica plate and a deformable mercury/electrolyte interface on a protuberant drop at a sealed capillary tube. When the mercury is negatively charged, the water forms a wetting film on mica, stabilized by electrical double layer forces. Mechanical perturbations are produced by driving the mica plate toward or by retracting the mica plate from the mercury surface. Electrical perturbations are applied to change the electrical double layer interaction between the mica and the mercury by imposing a step change of the bias voltage between the mercury and the bulk electrolyte. A theoretical model has been developed that can account for these observations quantitatively. Comparison between experiments and theory indicates that a no-slip hydrodynamic boundary condition holds at the molecularly smooth mica/electrolyte surface and at the deformable mercury/electrolyte interface. An analysis of the transient response based on the model elucidates the complex interplay between disjoining pressure, hydrodynamic forces, and surface deformations. This study also provides insight into the mechanism and process of droplet coalescence and reveals a novel, counterintuitive mechanism that can lead to film instability and collapse when an attempt is made to thicken the film by pulling the bounding mercury and mica phases apart.     

Coalescence of 3-phenyl-propynenitrile on Cu(111) into interlocking pinwheel chains

3-phenyl-propynenitrile (PPN) adsorbs on Cu(111) in a hexagonal network of molecular trimers formed through intermolecular interaction of the cyano group of one molecule with the aromatic ring of its neighbor. Heptamers of trimers coalesce into interlocking pinwheel-shaped structures that, by percolating across islands of the original trimer coverage, create the appearance of gear chains. Density functional theory aids in identifying substrate stress associated with the chemisorption of PPN's acetylene group as the cause of this transition.     

L-tryptophan radical cation electron spin resonance studies: connecting solution-derived hyperfine coupling constants with protein spectral interpretations

Fast-flow electron spin resonance (ESR) spectroscopy has been used to detect a free radical formed from the reaction of l-tryptophan with Ce (4+) in an acidic aqueous environment. Computer simulations of the ESR spectra from l-tryptophan and several isotopically modified forms strongly support the conclusion that the l-tryptophan radical cation has been detected by ESR for the first time. The hyperfine coupling constants (HFCs) determined from the well-resolved isotropic ESR spectra support experimental and computational efforts to understand l-tryptophan's role in protein catalysis of oxidation-reduction processes. l-Tryptophan HFCs facilitated the simulation of fast-flow ESR spectra of free radicals from two related compounds, tryptamine and 3-methylindole. Analysis of these three compounds' beta-methylene hydrogen HFC data along with equivalent l-tyrosine data has led to a new computational method that can distinguish between these two amino acid free radicals in proteins without dependence on isotope labeling, electron-nuclear double resonance, or high-field ESR. This approach also produces geometric parameters (dihedral angles for the beta-methylene hydrogens) that should facilitate protein site assignment of observed l-tryptophan radicals as has been done for l-tyrosine radicals.     

Silicone-grease-based immobilisation method for the preparation of enzyme electrodes

An approach to the construction of amperometric biosensors based on the incorporation of an enzyme in silicone grease and using the grease to fill micropores on a graphite surface is described. The enzyme-grease electrode concept, illustrated with the enzyme tyrosinase, offers a very simple, rapid and inexpensive approach to the fabrication of enzyme electrodes. The tyrosinase electrode responds very rapidly to dynamic changes in the concentration of phenolic compounds. A response time (t95%) as low as 5 s has been determined. With flow injection, 120 samples per hour can be processed with a relative standard deviation of 2.4%. The electrode remains active for about 12 d. The detection limit for dopamine is 6 x 10(-6) M. This method of biosensor construction should be applicable to other enzyme-substrate systems.     

Two-dimensional correlation gel permeation chromatography (2D GPC) study of the CH<Subscript>3</Subscript>SO<Subscript>3</Subscript>H-catalyzed polymerization of triethoxysilyl-terminated polystyrene. Molecular weight effect on the aggregate–aggregate interactions

The two-step polymerization process of two well-defined polymeric silane coupling agents, triethoxysilyl-terminated polystyrene with molecular weights equal to 2400 [TESi-PS (2400)] and 8000 [TESi-PS (8000)], catalyzed by 0.1 mol/kg CH₃SO₃H, was traced as a function of reaction time using gel-permeation chromatography (GPC). Two sets of GPC traces, collected during the condensation, were then converted to two-dimensional (2D) correlation spectra by using generalized 2D correlation theory. The 2D correlation spectra elucidated details of the aggregate–aggregate correlations [in particular, the difference between the correlations of TESi-PS (2400) and TESi-PS (8000)], thus demonstrating the effect of aggregation on the polymerization.     

Linear functionalized polyethylene prepared with highly active neutral Ni(II) complexes

Neutral Ni(II) salicylaldimine catalysts (pendant ligand = NCMe or PPh₃) were used to copolymerize ethylene with monomers containing esters, alcohols, anhydrides, and amides and yielded linear functionalized polyethylene in a single step. α‐Olefins and polycyclic olefin comonomers carrying functionality were directly incorporated into the polyethylene backbone by the catalysts without any cocatalyst, catalyst initiator, or other disturber compounds. The degree of comonomer incorporation was related to the monomer structure: tricyclononenes > norbornenes > α‐olefins. A wide range of comonomer incorporation, up to 30 mol %, was achieved while a linear polyethylene structure was maintained under mild conditions (40 °C, 100 psi ethylene). Results from the characterization of the copolymers by solution and solid‐state NMR techniques, thermal analysis, and molecular weight demonstrated that the materials contained a relatively pure microstructure for a functionalized polyethylene that was prepared in one step with no catalyst additive. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 2842–2854, 2002     

Unexpected Crosslinking and Diglycation as Advanced Glycation End-Products from Glyoxal

Glyoxal-derived advanced glycation end-products (AGEs) are formed in physiological systems affecting protein/peptide function and structure. These AGEs are generated during aging and chronic diseases such as diabetes and are considered arginine glycating agents. Thus, the study of glyoxal-derived AGEs in lysine residues and amino acid competition is addressed here using acetylated and non-acetylated undecapeptides, with one arginine and one lysine residue available for glycation. Tandem mass spectrometry results from a Fourier transform ion cyclotron resonance mass spectrometer showed glycated species at both the arginine and lysine residues. One species with the mass addition of 116.01096 Da is formed at the arginine residue. A possible structure is proposed to explain this finding (Nδ-[2-(dihydroxymethyl)-2H,3aH,4H,6aH-[1, 3]dioxolo[5,6-d]imidazolin-5-yl]-L-ornithine-derived AGE). The second species corresponded to intramolecular crosslink involving the lysine residue and its presence is checked with ion-mobility mass spectrometry. Graphical Abstract

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