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Patrick F James

Publications and source records attributed to Patrick F James.

7 recordsLinked to original sources
PubMed2006

Sources of artefacts in the electrospray ionization mass spectra of saturated diacylglycerophosphocholines: from condensed phase hydrolysis reactions through to gas phase intercluster reactions.

The mass spectra of diacylglycerophosphocholine phospholipids comprised of saturated fatty acids (1,2-dipentanoyl-sn-glycero-3-phosphocholine (D5PC); 1,2-dihexanoyl-sn-glycero-3-phosphocholine (D6PC), and 1,2-dimyristoyl-sn-glycero-3-phosphocholine (D14PC)) are sensitive to the electrospray ionization (ESI) conditions. When fresh solutions of phospholipid in 10 mM ammonium acetate are subjected to ESI, protonated oligomeric clusters, [DxPCn + H]+ (x = 5, 6, and 14) are observed in the following different types of mass spectrometers: 3D-quadrupole ion trap; linear ion trap, and triple quadrupole. The formation of the protonated cluster ions is not unique to the ion trap instruments, although they tend to be more abundant in these instruments. As the ESI solutions age, new ions are observed, which correspond to acid-catalyzed solution phase deacylation reactions. The collision induced dissociation fragmentation reactions of the oligomer cluster ions exhibit a distinct dependence on the cluster size, with the larger clusters (n > 2) simply fragmenting via the loss of lipid monomers. In contrast, the fragmentation of the dimeric cluster ion is unique, resulting in a number of additional reactions including covalent bond formation via intermolecular cluster SN2 reactions and SN2 transfer of a methyl group. The nature of the charge has a significant role in the formation of products via these intermolecular cluster reactions. Changing the head group to phosphoethanolamine "switches off" the SN2 reactions, while changing the cation from a proton to either a sodium or a potassium ion, diminishes the intermolecular reactions relative to monomer loss. Semi empirical PM3 calculations on [D6PC2 + H]+ suggest that the SN2 reactions are thermodynamically favored over simple monomer loss. These results have important implications in the field of lipidomics.

Artifacts↗
PubMed2004

Gas-phase synthesis and reactivity of the organomagnesates [CH3MgL2]- (L = Cl and O2CCH3): from ligand effects to catalysis.

Multistage mass spectrometry experiments combined with density functional theory (DFT) calculations were used to examine the gas-phase synthesis and ion-molecule reactions of the organomagnesates [CH(3)MgL(2)](-) (L = Cl and O(2)CCH(3)). Neutral species containing an acidic proton (HX) react with the [CH(3)MgL(2)](-) ions via addition with concomitant elimination of methane to form [XMgL(2)](-) ions. Kinetic measurements combined with DFT calculations revealed reduced reactivity of [CH(3)Mg(O(2)CCH(3))(2)](-) toward water, caused by the bidentate binding mode of acetate, which induces overcrowding of the Mg coordination sphere. The [CH(3)MgL(2)](-) ions reacted with (i) aldehydes with enolizable protons via enolization rather than the Grignard reaction and (ii) CH(3)CO(2)H to complete a catalytic cycle for the decarboxylation of acetic acid. Other electrophilic reagents such as pivaldehyde, benzaldehyde, methyl iodide, and trimethylborate are unreactive. DFT calculations on the competition between enolization and the Grignard reaction for [CH(3)MgCl(2)](-) ions reacting with acetaldehyde suggest that while the latter has a smaller barrier, it is entropically disfavored.

Journal Article↗
PubMed2004

Dimethyl cuprate undergoes C-C bond coupling with methyliodide in the gas phase but dimethyl argenate does not.

Multistage mass spectrometry experiments have been used to synthesize and study the reactions of (CH3)2M-(M = Cu and Ag) with methyl iodide in the gas phase. While the dimethylcuprate ion (M = Cu) reacts with CH3I via C-C bond cross coupling, its silver congener is unreactive. The experimental results are consistent with MP2/6-31++G** ab initio calculations, which reveal that the preferred mechanism for Cu involves the formation of a T-shaped Cu transition state. [reaction: see text]

Journal Article↗
PubMed2003

Gas phase ion chemistry of charged silver(I) adenine ions via multistage mass spectrometry experiments and DFT calculations.

Electrospray ionization (ESI) of solutions containing adenine and AgNO(3) yields polymeric [Ad(x)+ Ag(y)-zH]((y-z)+) species. Density functional theory (DFT) calculations have been used to examine potential structures for several of the smaller ions while multistage mass spectrometry experiments have been used to probe their unimolecular reactivity (via collision-induced dissociation (CID)) and bimolecular reactivity (via ion-molecule reactions with the neutral reagents acetonitrile, methanol, butylamine and pyridine). DFT calculations of neutral adenine tautomers and their silver ion adducts provide insights into the binding modes of adenine. We find that the most stable [Ad + Ag](+) ion does not correspond to the most stable neutral adenine tautomer, consistent with previous studies that have shown that transition metal ions can stabilize rare tautomeric forms of nucleobases. Both the charge and the stoichiometry of the [Ad(x)+ Ag(y)-zH]((y-z)+) complexes play pivotal roles in directing the types of fragmentation and ion-molecule reactions observed. Thus, [Ad(2)+ Ag(2)](2+) is observed to dissociate to [Ad + Ag](+) and to react with butylamine via proton transfer, while [Ad(2)+ Ag(2)- H](+) fragments via loss of neutral adenine to form the [Ad + Ag(2)- H](+) ion and does not undergo proton transfer to butylamine. DFT calculations on several isomeric [Ad(2)+ Ag(2)](2+) ions suggest that planar centrosymmetric cations, in which two adjacent silver atoms are bridged by two N7H adenine tautomers via N(3),N(9)-bidentate interactions, are the most stable. The [Ad + Ag(2)-H](+) ion adds two neutral reagents in ion-molecule reactions, consistent with the presence of two vacant coordination sites. It undergoes a silver atom loss to form the [Ad + Ag - H](+) radical cation, which in turn fragments quite differently to the even electron [Ad + Ag](+) ion. Several other pairs of radical cation/even electron adenine-silver complexes were also found to undergo different fragmentation reactions.

Journal Article↗
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Hospital versus home.

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Colonic Neoplasms↗