Identification of tyrosine nitration in UCH-L1 and GAPDH

Protein tyrosine nitration is a post-translational modification commonly used as a marker of cellular oxidative stress associated with numerous pathophysiological conditions. We focused on ubiquitin carboxyl terminal hydrolase-L1 (UCH-L1) and glyceraldehyde-3-phosphate (GAPDH) which are high-abundant brain proteins that have been identified to be highly susceptible to oxidative modification. Both UCH-L1 and GAPDH have been linked to the pathogenesis of Alzheimer's and Parkinson's disease, however specific nitration sites have not been elucidated. Identification of specific nitration sites and quantitation of endogenous nitrated proteins are important in correlating this modification to disease pathology. In this study, purified UCH-L1 and GAPDH were nitrated in vitro with peroxynitrite and the presence of nitrated proteins was confirmed by anti-3-nitrotyrosine Western blots. Data-dependent LC-MS/MS analysis identified several distinct tyrosine nitration sites in UCH-L1 (Tyr-80) and GAPDH (Tyr-47, Tyr-92, and Tyr-312). Subsequent validation with synthetic peptides was conducted for selected nitropeptides. An LC-MS/MS method was developed for semi-quantitative determination of the synthetic nitropeptides: KGQEVSPKVY(*) (UCH-L1) and mFQY(*) DSTHGKF (GAPDH). The nitropeptides were detectable in the mid-attomole range and the peak area response was linear over three orders of magnitude. Targeted analysis of endogenous UCH-L1 and GAPDH nitration was then conducted in an in vivo second-hand smoke rat model to evaluate the utility of this approach.     

The effect of boric acid on the vapour liquid equilibrium of aqueous potassium carbonate

Aqueous potassium carbonate has seen renewed interest as a viable solvent for pre and post combustion carbon capture and storage. However, slow reaction kinetics may require the addition of a rate promoter such as boric acid to improve efficiency. The vapour liquid equilibrium of 30 weight percent potassium carbonate with 0, 3 and 5 weight percent boric acid was investigated at 50 and 70 °C using a dynamic inert gas stripping method. By estimating the boric acid reactions an Electrolyte-NRTL model was able to fit this data and literature results very closely.     

Furan-oxidation-triggered inducible DNA cross-linking: acyclic versus cyclic furan-containing building blocks--on the benefit of restoring the cyclic sugar backbone

Oligodeoxynucleotides incorporating a reactive functionality can cause irreversible cross-linking to the target sequence and have been widely studied for their potential in inhibition of gene expression or development of diagnostic probes for gene analysis. Reactive oligonucleotides further show potential in a supramolecular context for the construction of nanometer-sized DNA-based objects. Inspired by the cytochrome P450 catalyzed transformation of furan into a reactive enal species, we recently introduced a furan-oxidation-based methodology for cross-linking of nucleic acids. Previous experiments using a simple acyclic building block equipped with a furan moiety for incorporation into oligodeoxynucleotides have shown that cross-linking occurs in a very fast and efficient way and that substantial amounts of stable, site-selectively cross-linked species can be isolated. Given the destabilization of duplexes observed upon introduction of the initially designed furan-modified building block into DNA duplexes, we explore here the potential benefits of two new building blocks featuring an extended aromatic system and a restored cyclic backbone. Thorough experimental analysis of cross-linking reactions in a series of contexts, combined with theoretical calculations, permit structural characterization of the formed species and allow assessment of the origin of the enhanced cross-link selectivity. Our experiments clearly show that the modular nature of the furan-modified building blocks used in the current cross-linking strategy allow for fine tuning of both yield and selectivity of the interstrand cross-linking reaction.     

Gold(III) chloride catalysed synthesis of 5-alkylidene-dihydrothiazoles

A two step synthesis of dihydrothiazoles is presented. First, the previously unknown N-propargylic dithiocarboimidates are produced in good yields from easily available, cheap starting materials. The subsequent gold catalysed ring closure is fast and efficient, leading to dihydrothiazoles through a cascade of 5-exo-dig cyclisation and 1,3-alkyl migration. The yields range from 74% to 95%.     

The formal [4+3] cycloaddition between donor-acceptor cyclobutanes and nitrones

The formal [4+3] cycloaddition of 2-alkoxy-1,1-dicarboxylate activated donor-acceptor cyclobutanes with nitrones is disclosed. The reaction forms structurally unique oxazepines in moderate to high yield with a wide scope of nitrones. In most cases either a diastereomeric mixture or a single diastereomer may be formed, depending on the reaction conditions.     

A local hermitian RBF meshless numerical method for the solution of multi‐zone problems

The local Hermitian interpolation (LHI) method is a strong‐form meshless numerical technique in which the solution domain is covered by a series of small and heavily overlapping radial basis function (RBF) interpolation systems. Aside from its meshless nature and the ability to work on very large scattered datasets, the main strength of the LHI method lies in the formation of local interpolations, which themselves satisfy both boundary and governing PDE operators, leading to an accurate and stable reconstruction of partial derivatives without the need for artificial upwinding or adaptive stencil selection. In this work, an extension is proposed to the LHI formulation which allows the accurate capture of solution profiles across discontinuities in governing equation parameters. Continuity of solution value and mass flux is enforced between otherwise disconnected interpolation systems, at the location of the discontinuity. In contrast to other local meshless methods, due to the robustness of the Hermite RBF formulation, it is possible to impose both matching conditions simultaneously at the interface nodes. The procedure is demonstrated for 1D and 3D convection–diffusion problems, both steady and unsteady, with discontinuities in various PDE properties. The analytical solution profiles for these problems, which experience discontinuities in their first derivatives, are replicated to a high degree of accuracy. The technique has been developed as a tool for solving flow and transport problems around geological layers, as experienced in groundwater flow problems. The accuracy of the captured solution profiles, in scenarios where the local convective velocities exceed those typically encountered in such Darcy flow problems, suggests that the technique is indeed suitable for modeling discontinuities in porous media properties. © 2010 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq 27: 1201–1230, 2011     

Understanding the complex dissociation dynamics of energy selected dichloroethylene ions: neutral isomerization energies and heats of formation by imaging photoelectron-photoion coincidence

The dissociative photoionization of 1,1-C(2)H(2)Cl(2), (E)-1,2-C(2)H(2)Cl(2), and (Z)-1,2-C(2)H(2)Cl(2) has been investigated at high energy and mass resolution using the imaging photoelectron photoion coincidence instrument at the Swiss Light Source. The asymmetric Cl-atom loss ion time-of-flight distributions were fitted to obtain the dissociation rates in the 10(3) s(-1) < k < 10(7) s(-1) range as a function of the ion internal energy. The results, supported by ab initio calculations, show that all three ions dissociate to the same C(2v) symmetry ClC═CH(2)(+) product ion. The 0 K onset energies thus establish the relative heats of formation of the neutral isomers, that is, the isomerization energies. The experimental rate constants, k(E), as well as ab initio calculations indicate an early isomerization transition state and no overall reverse barrier to dissociation. The major high energy channels are the parallel HCl loss and the sequential ClC═CH(2)(+) → HCCH(+) + Cl process, the latter in competition with a ClC═CH(2)(+) → ClCCH(+) + H reaction. A parallel C(2)H(2)Cl(2)(+) → C(2)HCl(2)(+) + H channel also weakly asserts itself. The 0 K onset energy for the sequential Cl loss reaction suggests no barrier to the production of the most stable acetylene ion product; thus the sequential Cl-atom loss is preceded by a ClC═CH(2)(+) → HC(Cl)CH(+) reorganization step with a barrier lower than that of the second Cl-atom loss. The breakdown diagram corresponding to this sequential dissociation reveals the internal energy distribution of the first C(2)H(2)Cl(+) daughter ion, which is determined by the kinetic energy release in the first, Cl loss reaction at high excess energies. At low kinetic energy release, this distribution corresponds to the predicted two translational degrees of freedom, whereas at higher energies, the excess energy partitioning is characteristic of only one translational degree of freedom. New Δ(f)H(o)(298K) of 3.7, 2.5, and 0.2 ± 1.75 kJ mol(-1) are proposed for 1,1-C(2)H(2)Cl(2), (E)-1,2-C(2)H(2)Cl(2), and (Z)-1,2-C(2)H(2)Cl(2), respectively, and the proton affinity of ClCCH is found to be 708.6 ± 2.5 kJ mol(-1).     

Fluorescence self-quenching in aromatic vapours; the role of excited dimers

At temperatures sufficiently high to produce an appreciable pressure of 9, 10-diphenylanthracene, perylene or pyrene, the quantum yield of fluorescence is found to be independent of vapour pressure. The negative temperature coefficient of self-quenching in anthracene vapour is explained in terms of the dissociation of an excited dimer which is also responsible for delayed fluorescence.

The pressure-dependence of the excited dimer lifetime at low pressures is shown to be consistent with a pressure-independent quenching constant if the second-order dissociation of the excited dimer becomes first-order at higher pressures.     

The collisional stabilization of excited β-naphthylamine molecules by the paraffin hydrocarbons in the gas phase

The transfer of vibrational energy from molecules of β-naphthylamine excited by the mercury lines at 2804 Å and 2652 Å to the homologous series of paraffin hydrocarbons up to n-hexane has been investigated in the gas phase at 180°C. Although the average amount of energy transferred collisionally increases with the complexity of the added gas by a factor of 5, the transfer efficiency expressed as an accommodation coefficient remains virtually unchanged.

A transfer mechanism based on the internal redistribution of vibrational energy within the collision complex is examined, in terms of which it is unnecessary to invoke vibration-vibration transfer except for pentane and hexane. The collision duration estimated on the basis of this model is well within an order of magnitude of that expected from collision diameters and relative velocities of the molecules concerned.     

H-atom abstraction dynamics of reactions between Cl atoms and heterocyclic organic molecules

The HCl(v' = 0, J') rotational state distributions produced in the photoinitiated reactions of ground spin-orbit state Cl(2P3/2) atoms with the organic heterocycles oxirane (c-C2H4O), thiirane (c-C2H4S) and oxetane (c-C3H6O) have been measured using the technique of 2 + 1 resonance-enhanced multiphoton ionization in a time-of-flight mass spectrometer. In contrast to previous studies of H-atom abstraction dynamics by Cl atoms with linear functionalized molecules, the nascent HCl(v' = 0, J') products of the reactions of the three-membered heterocycles oxirane and thiirane are formed rotationally cold, with mean rotational energies <Erot> of (0.28 ± 0.02) kcal mol-1 and (0.31 ± 0.02) kcal mol-1, respectively. The reaction of Cl atoms with the four-membered heterocycle oxetane, however, results in more rotationally excited HCl(v' = 0, J') products for which <Erot> = (0.78 ± 0.03) kcal mol-1. Ab initio calculations were performed at the G2//MP2/6-311G(d,p) level to characterize molecular complexes and transition states on the reactive pathways. In all cases, the reactions were calculated to be barrierless, and weakly bound pre- and post-reaction complexes were located on the potential energy surfaces. The observed distributions and calculated reaction profiles are compared with previous studies of the reactions of Cl atoms with linear functionalized organic molecules and the consequences of the constrained molecular geometry on the HCl(v' = 0, J') rotational distribution discussed in terms of the dipole-dipole interaction model proposed previously.