School of Chemistry journal papers published in 2008

1. L. O'Donovan, M. P. Carty and F. Aldabbagh. RSC Prospect: "First Synthesis of N-[(Aziridinyl-2-yl)methyl]Benzimidazolequinone and Analysis of Toxicity Towards Normal and Fanconi Anemia Cells. Chemical Communications 2008, 5592-5594.

2. F. Aldabbagh, P. B. Zetterlund, M. Okubo, Nitroxide-Mediated Precipitation Polymerization of Styrene in Supercritical Carbon Dioxide: Effect of Monomer Loading and Nitroxide Partitioning on Control. European Polymer Journal, 2008, 44, 4037-4046.

3. O. Gibbons, W. M. Carroll, F. Aldabbagh, P. B. Zetterlund, B. Yamada. Nitroxide-Mediated Radical Polymerization of N-tert-Butylacrylamide. Macromolecular Chemistry and Physics 2008, 209, 2434-2444.

4. K. Fahey and F. Aldabbagh. Synthesis of Seven and Eight-Membered [1,2-a] Alicyclic Ring-Fused Benzimidazoles and 3-Azirdinylazepino[1,2-a]benzimidazolequinone as a Potential Antitumor Agent. Tetrahedron Letters 2008, 49, 5235-5237.

5. S. Hehir, L. O'Donovan, M. P. Carty, F. Aldabbagh. Synthesis of Dimethyl Substituted Benzimidazoles Containing Cyclopropane Fused onto Five to Eight Membered [1,2-a] Alicyclic Rings and Influence of Methyl Group Substituents on Cytotoxicity of Benzimidazolequinones. Tetrahedron 2008, 64, 4196-4203.

6. F. Aldabbagh, P. B. Zetterlund, M. Okubo. Improved Control in Nitroxide-Mediated Radical Polymerization Using Supercritical Carbon Dioxide. Macromolecules 2008, 41, 2732-2734.

7. Invited Review: Fawaz Aldabbagh in Comprehensive Heterocyclic Chemistry III, Alan R. Katritzky Exec Ed; Christopher A Ramsden, Eric F. V. Scriven, and Richard J. K. Taylor Ed; Elsevier; Ray C. F. Jones, Vol. Ed; Volume 10, Chapter 10.13, Bicyclic 5-6 Systems: Five Heteroatoms 2:3 or 3:2, pp 661-702. (ISBN 978-0-08-045002-5).

8. J. Ryan, F. Aldabbagh, P. B. Zetterlund, B. Yamada. Nitroxide-Mediated Controlled/Living Radical Copolymerizations with Macromonomers. Reactive and Functional Polymers 2008, 68, 692-700.

9. R. N. Butler, J. M. Hanniffy, J. C. Stephens, and L. A. Burke, A Ceric Ammonium Nitrate N-Dearylation of N-p-Anisylazoles Applied to Pyrazole, Triazole, Tetrazole, and Pentazole Rings: Release of Parent Azoles. Generation of Unstable Pentazole, HN5/N5-, in Solution. J. Org. Chem. 2008, 73, 1354-1364.

10. B. O'Brien J. S. Stinson and W. M. Carroll. Development of a New Niobium-based Alloy for Vascular Stent Applications. Journal of the Mechanical Behavior of Biomedical Materials. 2008, 1(4), 303-312

11. B. O'Brien, J. S. Stinson, D. A. Boismier and W. M. Carroll. Characterization of an NbTaWZR Alloy Designed for Magnetic Resonance Angiography Compatible Stents. Biomaterials. 2008, 29(34), 4540.

12. H. Gallaher W. M.  Carroll, M. Dowd and Y. Rochev. The Effects of Vindblastine on Endothelial Cells. Endothelium. 2008, 15(1), 9-15.

13. M. Burke, B.  Clarke, Y. Rochev, A. Gorelov and W. M. Carroll. Estimation of the Strength of Adhesion Between a Thermoresponsive Polymer Coating and Nitinol Wire. Journal of Materials Science:  Materials in Medicine. 2008, 19(5), 1971-1979.

14. B. O’Brien, J. S. Stenson, J. and W. M. Carroll. Initial Exploration of Ti-Ta, Ti-Ta-Ir and Ti-Ir alloys; Candidate materials for Coronary Stents. Acta Biomaterialia. 2008, 4, 1553-1559.

15. E. McLucas, Y. Rochev, W. M. Carroll and T. J. Smith. Analysis of the Effects of Surface Treatments on Nickel Release from Nitinol Wires and their Impact on Candidate Gene Expression in Endothelial Cells. Journal of Materials Science: Materials in Medicine. 2008, 19(3), 975-980.

16. S. Yanagisawa, P. B. Crowley, S. J. Firbank, A. T. Lawler, D. M. Hunter, W. McFarlane. C. Li, T. Kohzuma, M. J. Banfield, C. Dennison. pi-interaction tuning of the active site properties of metalloproteins. J. Am. Chem. Soc. 2008, 130, 15420-15428.

17. M. V. Petoukhov, J. B. Vicente, P. B. Crowley, M. A. Carrondo, M. Teixeira and D. I. Svergun. Quaternary structure of flavorubredoxin as revealed by synchrotron radiation small-angle X-ray scattering. Structure 2008, 16, 1428-1436.

18. P. B. Crowley, P. M. Matias, H. Mi, S. J. Firbank, M. J. Banfield and C. Dennison. Regulation of Protein Function: Crystal Packing Interfaces and Conformational Dimerization. Biochemistry 2008, 47, 6583–6589.

19. P. B. Crowley, P. Ganji, H. Ibrahim. Protein surface recognition: structural characterisation of cytochrome c-porphyrin complexes. Chembiochem., 2008, 9, 1029-33.

20. P. B. Crowley, K.  Brett, J. Muldoon. NMR spectroscopy reveals cytochrome c-poly(ethylene glycol) interactions. ChemBioChem. 2008, 9, 685-8.

21. A. M. El-Nahas, J. M. Simmie, M. V. Navarro, J. W. Bozzelli, G. Black, H. J. Curran. Thermochemistry and kinetics of acetonylperoxy radical isomerisation and decomposition: a quantum chemistry and CVT/SCT approach. Phys. Chem. Chem. Phys., 2008, 10, 139–7149.

22. D. Healy, H. J. Curran, J. M. Simmie, D.M. Kalitan, C. M. Zinner, A. B. Barrett, E. L. Petersen, and G. Bourque. Methane/Ethane/Propane Mixture Oxidation at High Pressures and at High, Intermediate and Low Temperatures. Combustion and Flame 2008, 155(3), 441–448.

23. D. Healy, H. J. Curran, S. Dooley, J. M. Simmie, D. M. Kalitan, E. L. Petersen, and G. Bourque. Methane/Propane Mixture Oxidation at High Pressures and at High, Intermediate and Low Temperatures. Combustion and Flame 2008, 155(3), 451–461.

24. J. Aguilera-Iparraguirre, H. J. Curran, W. Klopper, J. M. Simmie. Accurate Benchmark Calculation of the Reaction Barrier Height for Hydrogen Abstraction by the Hydroperoxyl Radical from Methane. Implications for CnH 2n+2 where n = 2 -4. Journal of Physical Chemistry A. 2008, 112(30), 7047–7054.

25. J. M. Simmie, G. Black, H. J. Curran, J. P. Hinde. Enthalpies of formation and Bond Dissociation Energies of Lower Alkyl Hydroperoxides and Related Hydroperoxy and Alkoxy Radicals. Journal of Physical Chemistry A. 2008, 112(22), 5010–5016.

26. J. Simmie, W. K. Metcalfe, H. J. Curran. Ketene Thermochemistry. Chem.Phys.Chem., 2008, 9(5), 700–702.

27. S. M. Gallagher, H. J. Curran, W. K. Metcalfe, D. Healy, J. M. Simmie and G. Bourque. A rapid compression machine study of the oxidation of propane in the negative temperature coefficient regime. Combustion and Flame, 2008, 153(1-2), 316–333.

28. S. Dooley, H. J. Curran, J. M. Simmie. Autoignition measurements and a validated kinetic model for the biodiesel surrogate, methyl butanoate. Combustion and Flame, 2008, 153(1-2), 2–32.

29. R. B. Zhang, K. Zhang and L. A. Eriksson, Theoretical Study of Damage of 3’-Uridine Monophosphate Induced by Electron Attachment. Chem. Eur. J., 2008, 14, 2850-2856.

30. V. Labet, A. Grand, C. Morell, J. Cadet and L. A. Eriksson. Proton Catalysed Hydrolytic Deamination of Cytosine – A Computational Study, (N. Russo Festschrift) Theor. Chem. Acc., 2008, 120, 429-435.

31. E. Erdtman and L. A. Eriksson. Mechanism of 5-aminolevulinic acid tautomerism – a novel self-catalyzed mechanism. J. Phys. Chem. A. 2008, 112, 4367-4374.

32. E. S. E. Eriksson, R. C. Guedes and L. A. Eriksson. Redox and debromination reactions of brominated hypericin. Int. J. Quantum Chem., 2008, 108, 1021-1029.

33. V. Labet, A. Grand, J. Cadet and L. A. Eriksson. Deamination of the radical cation of the base moiety of 2’deoxycytidine: A theoretical study. ChemPhysChem, 2008, 9, 1195-1203.

34. M. Karlsson, Å. Strid, A. Sirsjö and L. A. Eriksson. Homology models and Molecular Modeling of Human Retinoic Acid Metabolizing Enzymes Cytochrome P450 26A1 (CYP26A1) and P450 26B1 (CYP26B1). J. Chem. Theory Comput., 2008, 4, 1021-1027.

35. P. Schyman, L. A. Eriksson, R. B. Zhang and A. Laaksonen. Hydroxyl radical - thymine adduct induced DNA damages. Chem. Phys. Letters, 2008, 458, 186-189.

36. S. Jönsson, L. A. Eriksson and B. van Bavel, Multivariate characterization of nitroaromatic compounds. Analytica Chimica Acta. 2008, 621, 155-162.

37. E. Erdtman, D. J. V. A. dos Santos, L. Löfgren and L. A. Eriksson. Properties of 5-aminolevulinic acid and its alkyl esters in a lipid bilayer model. Che m. Phys Letters, 2008, 463, 178–182.

38. K. A. K. Musa and L. A. Eriksson. Photochemistry and degradation of Naproxen and the active metabolite of Nabumetone. J. Phys. Chem. A, 2008, 112, 10921-10930.

39. M. Pellisier, F. Barriere, A. J. Downard, D. Leech. Improved stability of redox enzyme layers on glassy carbon electrodes via covalent grafting, Electrochem. Comm. 2008, 10, 835–838.

40. S. Boland, F. Barriere and D. Leech. Designing Stable Redox-Active Surfaces: Chemical Attachment of an Osmium Complex to Glassy Carbon Electrodes Prefunctionalized by Electrochemical Reduction of an In Situ-Generated Aryldiazonium Cation. Langmuir 2008, 24, 6351–6358.

41. P. Kavanagh, P. Jenkins and D. Leech. Electroreduction of O2 at a mediated Melanocarpus albomyces laccase cathode in a physiological buffer, Electrochem. Comm. 2008, 10, 970-972.

42. S. Boland, P. Kavanagh, D. Leech. Mediated enzyme electrodes for biological fuel cell and biosensor applications. ECS Transactions. 2008, 13, 77-87.

43. Book Chapter: D. Leech, M. Pellissier, F. Barrière. "Powering fuel cells through biocatalysis” in Electrochemical Sensors, Biosensors and their Biomedical Applications, X. Zhang, H. Ju, J. Wang (eds), Academic Press, 2008. pp. 385–410. ISBN: 978-0-12-373738-0. 10.1016/B978-012373738-0.50014-3.

44. Synthesis of novel migrastatin and dorrigocin A analogues from D-glucal. G. Anquetin, S. L. Rawe, K. McMahon, E. Murphy and P. V. Murphy. Chem. Eur. J. 2008, 14, 1592–1600.

45. Y. Zhou, Y. Zhao, K. M. O’ Boyle and P. V. Murphy. Hybrid angiogenesis inhibitors: synthesis and biological evaluation of bifunctional compounds comprised of 1-deoxynojirimycin and 5-aryl-1,2,3-triazoles. Bioorganic and Medicinal Chemistry Letters, 2008, 18, 954-8.

46. G. Anquetin, G. Horgan, S. Rawe, D. Murray, A. Madden, P. MacMathuna, P. Doran and P. V. Murphy. Synthesis of Novel Macrolactam and Macroketone Analogues of Migrastatin from D-Glucal and Comparison with Macrolactone and Acyclic Analogues: A Dorrigocin A Congener is a Potent Inhibitor of Gastric Cancer Cell Migration. European Journal of Organic Chemistry. 2008, 11, 1953-1958.

47. V. Chagnault, J. Lalot and P. V. Murphy. Synthesis of somatostatin mimetics based on 1-deoxynojirimycin. ChemMedChem, 2008, 3(7):1071-1076.

48. Y. Zhao, Y. Zhou, K. M. O’ Boyle and P. V. Murphy. Hybrids of 1-deoxynojirimycin and aryl-1,2,3-triazoles and biological studies related to angiogenesis. Bioorganic and Medicinal Chemistry, 2008, 16, 6333–6337.

49. D. Doyle and P. V. Murphy. Synthesis of novel glycophanes derived from glucuronic acid by ring closing alkene and alkyne metathesis. Carbohydrate Res. 2008, 343, 2535-2544.

50. Y. Zhou and P. V. Murphy. New access to 1-deoxynojirimycin derivatives via azide-alkene cycloaddition. Organic Letters, 2008, 10, 3777–3780.

51. L. Batema, S. W. Breeden and P. O'Leary. New chiral diamide ligands: synthesis and application in allylic alkylation. Tetrahedron: Asymmetry. 2008, 391-396.

52. P. Owens, A. G. Ryder and N. J. F. Blamey. Frequency Domain Fluorescence Lifetime Study of Crude Petroleum Oils. Journal of Fluorescence. 2008, 18(5), 997-1006

53. N. J. F. Blamey, A. G. Ryder, M. Feely, P. Dockery, and P. Owens. The application of structured-light illumination to hydrocarbon-bearing fluid inclusions. Geofluids. 2008, 8(2), 102-112.

54. D. M. Togashi and A. G. Ryder. A fluorescence analysis of ANS bound to bovine serum albumin: binding properties revisited. Journal of Fluorescence. 2008. 18(2), 519-526.

55. S. Gaïl, P. Dagaut, G. Black, J. M. Simmie. Kinetics of 1,2-Dimethylbenzene Oxidation and Ignition: Experimental and Detailed Chemical Kinetic Modelling. Combustion Science & Technology, 2008, 180, 1748–1771.

56. R. Asatryan, J. W. Bozzelli and J. M. Simmie. Thermochemistry of Methyl and Ethyl Nitro, RNO2, and Nitrite, RONO, Organic Compounds. Journal of Physical Chemistry A. 2008, 112(14): 3172–3185.

57. W. J. Spillane, A. O’Byrne and C. J. A. McCaw. Elimination mechanisms in the aminolysis of sulfamate esters of the type NH2SO2OC6H4X-models of enzyme inhibitors. Eur. J. Org. Chem., 2008, 24, 4200-4205.

58. W. J. Spillane, D. P. Kelly, J.-B. Malaubier, G. G. Hanniffy, B. G. Feeney, C. C. Coyle, L. M. Kelly, E. F. Thompson, D. G. Concagh, M. B. Sheahan, Recent developments in structure-taste studies of sulfamates. ACS Symposium Series: Sweetness and Sweeteners, 2008, 979, 530-544.

59. W. J. Spillane, C. J. A. McCaw and N. P. Maguire, Kinetic and mechanistic studies of the hydrolysis of sulfamate esters: a non-elimination decomposition route. Tet. Lett., 2008, 49(6), 1049-1052.

60. R. Kadirvelraj, B. L. Foley, J. D. Dyekjær and R. J. Woods. Involvement of Water in Carbohydrate-Protein Binding: Concanavalin A Revisited. J. Am. Chem. Soc., 2008, 130, 16933-16942.

61. A. B. Yongye, J. Gonzalez-Outeriño, J. Glushka, V. Schutlheis, and R. J. Woods. The Conformational Properties of Methyl a-(2,8)- di/trisialoside. Implications for anti-Neisseria meningitidis Vaccine Design. Biochemistry. 2008, 47, 12493-12514.

62. O. Charvatova, B. L. Foley, M. Bern, J. Sharp, R. Orlando and R. J. Woods. Quantifying Protein Interface Footprinting by Hydroxyl Radical Oxidation and Molecular Dynamics Simulation: Application to Galectin-1. J. Am. Soc. Mass Spectrom. 2008, 19, 1692-1705.

63. M. L. DeMarco and R. J. Woods. Structural Glycobiology: A Game of Snakes and Ladders. Glycobiology (Invited Review), 2008, 18, 426-440.

64. A. B. Yongye, B. L. Foley and R. J. Woods. On achieving experimental accuracy from molecular dynamics simulations of flexible molecules: aqueous glycerol. J. Phys. Chem. A. 2008, 112, 2634-2639.

65. M. Seo, N. Castillo, R. Ganzynkowicz, C. R. Daniels,  R. J. Woods, P.-N. Roy and T. L. Lowary. An approach for the simulation and modeling of flexible rings.  Application to the α-D-arabinofuranoside ring, a key constituent of polysaccharides from Mycobacterium tuberculosis. J. Chem. Theory Comput., 2008, 4, 184-191

66. K. N. Kirschner, A. B. Yongye, S. M. Tschampel, J. Gonzalez Outeriño, C. R. Daniels, B. L. Foley and R. J. Woods. GLYCAM06: A Generalizable Biomolecular Force Field: Carbohydrates. J. Comput. Chem., 2008, 29, 622-655.

67. M. B. Tessier, M. L. DeMarco, A. B. Yongye and R. J. Woods. Extension of the GLYCAM06 Biomolecular Force Field to Lipids, Lipid Bilayers and Glycolipids. Molecular Simulation, 2008, 34, 349-364.

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