Biomedical subjects

Hadi Lioe

Publications and source records attributed to Hadi Lioe.

4 recordsLinked to original sources

PubMed2005

Neighbouring group processes in the deamination of protonated phenylalanine derivatives.

The gas-phase fragmentation of protonated phenylalanine and a series of its derivatives (tyrosine, 4-methylphenylalanine, 4-aminophenylalanine, 4-methoxyphenylalanine, 4-tert-butylphenylalanine, 4-fluorophenylalanine, 4-chlorophenylalanine, 4-bromophenylalanine, 4-iodophenylalanine, 4-cyanophenylalanine, 4-nitrophenylalanine, 3-fluorophenylalanine, and 3,4-dichlorophenylalanine) were examined using a combination of low energy CID in a quadrupole ion trap mass spectrometer as well as DFT calculations and RRKM modelling. In particular, the relationship between the electron-donating ability of the substituent and the competitive losses of H2O + CO and NH3 were explored through the application of the Hammett equation. It was found that electron-donating substituents promote the loss of NH3, while electron-withdrawing substituents suppress the loss of NH3 and favour the H2O + CO loss fragmentation channel instead. These observations are consistent with a neighbouring group pathway operating for the loss of NH3. Molecular orbital calculation (at the B3LYP/6-31+G(d,p) level of theory) were also performed for a range of derivatives to compare the relative transition state energy barriers for three competing mechanisms: (i) the combined loss of H2O + CO, which is triggered by an initial intramolecular proton transfer from the ammonium group to hydroxyl OH, followed by the combined loss of H2O and CO to form an immonium ion; (ii) loss of NH3 via an aryl assisted neighbouring group pathway to yield a phenonium ion; (iii) loss of NH3 via a 1,2-hydride migration process, which results in the formation of a benzyl cation. The relative energy barriers for H2O + CO loss remain nearly constant, while that for both NH3 pathways increase as the substituent moves from electron-donating to electron-withdrawing. The relative transition state energy for loss of NH3 via the aryl assisted neighbouring group pathway is always lower than that of the 1,2-hydride migration process. RRKM modelling of the DFT predicted barrier heights suggest that the rate constants for H2O + CO loss are insensitive to the substituent on the ring, while the NH3 loss channels are greatly affected by the substituent. These theoretical results are consistent with the experimental observation of the relative yields of the competing fragmentation channels. Finally, comparisons with published gas phase and condensed phase studies on related systems are made.

Ammonia↗

PubMed2005

Atomic force microscopy study of the interaction between adsorbed poly(ethylene oxide) layers: effects of surface modification and approach velocity.

The interaction forces between layers of the triblock copolymer Pluronic F108 adsorbed onto hydrophobic radio frequency glow discharge (RFGD) thin film surfaces and hydrophilic silica, in polymer-free 0.15 M NaCl solution, have been measured using the atomic force microscope (AFM) colloid probe technique. Compression of Pluronic F108 layers adsorbed on the hydrophobic RFGD surfaces results in a purely repulsive force due to the steric overlap of the layers, the form of which suggests that the PEO chains adopt a brush conformation. Subsequent fitting of these data to the polymer brush models of Alexander-de Gennes and Milner, Witten, and Cates confirms that the adsorbed Pluronic F108 adsorbs onto hydrophobic surfaces as a polymer brush with a parabolic segment density profile. In comparison, the interaction between Pluronic F108 layers adsorbed on silica exhibits a long ranged shallow attractive force and a weaker steric repulsion. The attractive component is reasonably well described by van der Waals forces, but polymer bridging cannot be ruled out. The weaker steric component of the force suggests that the polymer is less densely packed on the surface and is less extended into solution, existing as polymeric isolated mushrooms. When the surfaces are driven together at high piezo ramp velocities, an additional repulsive force is measured, attributable to hydrodynamic drainage forces between the surfaces. In comparing theoretical predictions of the hydrodynamic force to the experimentally obtained data, agreement could only be obtained if the flow profile of the aqueous solution penetrated significantly into the polymer brush. This finding is in line with the theoretical predictions of Milner and provides further evidence that the segment density profile of the adsorbed polymer brush is parabolic. A velocity dependent additional stepped repulsive force, reminiscent of a solvation oscillatory force, is also observed when the adsorbed layers are compressed under high loads. This additional force is presumably a result of hindered drainage of water due to the presence of a high volume fraction of polymer chains between the surfaces.

Journal Article↗

PubMed2004

A mass spectrometric and molecular orbital study of H2O loss from protonated tryptophan and oxidized tryptophan derivatives.

Protonated N-acetyltryptophan, oxindolylalanine (a mono-oxidized derivative of tryptophan), and N-acetyloxindolylalanine, as well as several di- and tripeptide derivatives containing oxindolylalanine, undergo a range of fragmentation reactions in the gas phase, including the loss of water. In order to elucidate the sites of water loss within these ions, and to determine the mechanisms associated with these processes, we have conducted a series of experiments employing multistage tandem mass spectrometry (MS/MS and MS(3)) in a quadrupole ion trap mass spectrometer, regiospecific structural labeling, and independent solution-phase syntheses of proposed product ion structures, coupled with the use of molecular orbital calculations at the B3LYP/6-31G* level of theory. We demonstrate that the loss of H(2)O from the amide carbonyl group of protonated N-acetyltryptophan O-methyl ester occurs via a "side-chain-backbone" neighboring group reaction to yield a protonated carboline derivative. In contrast, the loss of water from the O-methyl ester of protonated oxindolylalanine results in the formation of a tricyclic structure by "backbone-side-chain" nucleophilic attack from the amino nitrogen to the C2 position of the indole ring. The O-methyl ester of protonated N-acetyloxindolylalanine was found to dissociate via the loss of water from both possible sites, i.e. from the side-chain indolyl oxygen and the backbone amide carbonyl group. An estimate of the relative preference for water loss from each site was obtained from the abundances of product ions formed from MS(3) analysis of regiospecifically labeled derivatives of N-acetyloxindolylalanine, and from the results of molecular orbital calculations. These studies indicate the absence of a characteristic 'signature' ion or neutral loss for peptides containing oxindolylalanine residues under low-energy ion trap CID conditions.

Models, Molecular↗

PubMed2004

Gas-phase reactions of protonated tryptophan.

The gas phase reactions of protonated tryptophan have been examined in a quadrupole ion trap using a combination of collision induced dissociation, hydrogen-deuterium exchange, regiospecific deuterium labeling and molecular orbital calculations (at the B3LYP/6-31G* level of theory). The loss of ammonia from protonated tryptophan is observed as the primary fragmentation pathway, with concomitant formation of a [M + H - NH(3)](+) ion by nucleophilic attack from the C3 position of the indole side chain. Hydrogen-deuterium exchange and regiospecific deuterium labeling reveals that scrambling of protons in the C2 and C4 positions of the indole ring, via intramolecular proton transfer from the thermodynamically preferred site of protonation at the amino nitrogen, precedes ammonia loss. Molecular orbital calculations have been employed to demonstrate that the activation barriers to intramolecular proton transfer are lower than that for NH(3) loss.

Gases↗