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Investigating the Reactions of Gas-Phase Radicals Using Distonic Ions Benjamin B

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Investigating the Reactions of Gas-Phase Radicals Using Distonic Ions Benjamin B University of Wollongong Research Online University of Wollongong Thesis Collection University of Wollongong Thesis Collections 2011 Investigating the reactions of gas-phase radicals using distonic ions Benjamin B. Kirk University of Wollongong, [email protected] Recommended Citation Kirk, Benjamin B., Investigating the reactions of gas-phase radicals using distonic ions, Doctor of Philosophy thesis, School of Chemistry, University of Wollongong, 2011. http://ro.uow.edu.au/theses/3374 Research Online is the open access institutional repository for the University of Wollongong. For further information contact the UOW Library: [email protected] Investigating the reactions of gas-phase radicals using distonic ions. A thesis submitted in fulfilment of the requirements for the award of the degree Doctor of Philosophy from The University of Wollongong by Benjamin B. Kirk BCompSci, BSci(Hons I) School of Chemistry 2011 CERTIFICATION I, Benjamin B. Kirk, declare that this thesis, submitted in fulfilment of the requirements for the award of Doctor of Philosophy, in the School of Chemistry, University of Wollongong, is wholly my own work unless otherwise referenced or acknowledged. The document has not been submitted for qualifications at any other academic institution. Benjamin B. Kirk 03 June 2011 CONTENTS Contents i List of Abbreviations v List of Figures vi List of Schemes xi List of Tables xiv 1 Introduction 5 1.1 Foreward . 5 1.2 Free radicals . 5 1.2.1 Generation of free radicals in the gas phase . 9 1.2.2 Detection and characterisation of free radicals in the gas phase . 12 1.2.3 Mass spectrometry . 16 1.3 Radical ions . 36 1.3.1 Distonic radical ions . 36 1.3.2 Distonic radical cations . 39 1.3.3 Distonic radical anions . 41 1.3.4 Structural characterisation of distonic ions . 44 1.3.5 Selective gas phase synthesis of distonic radical ions . 49 1.4 Distonic radical ions as models for neutral reactions . 54 1.5 Thesis overview . 57 2 Instrumentation 59 2.1 Introduction . 59 2.2 Photolysis . 60 i II CONTENTS 2.2.1 Modifications for laser photolysis . 64 2.2.2 Synthesis of radical ions by laser photolysis . 70 2.2.3 Summary . 84 2.3 Ion-molecule reactions . 85 2.3.1 Modifications for ion-molecule reactions . 86 2.3.2 Proof of principle ion-molecule reactions . 91 2.3.3 Calculating the concentration of a neutral . 92 2.3.4 Determining the concentration of dioxygen . 96 2.3.5 Measuring reaction kinetics . 96 2.3.6 Reaction efficiency . 97 2.3.7 Errors in calculated reaction rates . 98 2.4 Conclusion . 99 2.5 Materials . 100 2.5.1 General method for synthesising trimethylammonium iodide salts 100 2.5.2 General method for generation of iodides from alcohols . 101 3 Gas phase reactions of distonic phenyl radical ions 103 3.1 Introduction . 103 3.1.1 Degradation of the phenylperoxyl radical . 104 3.2 Method . 108 3.2.1 Mass spectrometry . 108 3.2.2 Computational methods . 109 3.2.3 Predicting relative reaction rates . 109 3.3 Materials . 111 3.3.1 Nitrogen dioxide . 111 3.3.2 N,N,N-trimethyl-4-nitrobenzaminium iodide . 111 3.4 Results . 112 3.4.1 Gas phase synthesis of distonic ion models for phenyl radical . 112 3.4.2 Comparison of distonic phenyl radical ions to the neutral analogue115 3.4.3 Structural characterisation of the distonic analogues . 116 3.4.4 Reaction of 4-(N,N,N-trimethylammonium)phenyl radical cation (1) with O2 ................................. 124 3.4.5 Reaction of 4-carboxylatophenyl radical anion (2) with O2 . 127 CONTENTS III 3.4.6 Charge-tag effects on the reaction of distonic phenyl radical ions with O2 ................................... 130 3.4.7 Discussion . 133 3.4.8 Kinetics of distonic phenyl radicals with O2 . 134 3.4.9 Calculation of the 4-carboxylatophenyl radical anion + O2 poten- tial energy surface . 138 3.5 Conclusion . 142 4 Gas phase reactions of distonic phenylperoxyl radicals with NOx 147 4.1 Introduction . 147 4.2 Methods . 152 4.2.1 Materials . 152 4.2.2 Mass spectrometry . 153 4.3 Results . 153 4.3.1 Reaction of the phenylperoxyl radical with NO· . 153 4.3.2 Reaction of the alkylperoxyl radicals with NO· . 159 · 4.3.3 Reaction of the phenylperoxyl radical with NO2 . 161 4.4 Conclusion . 163 5 Gas phase reactions of cyclohexyl radicals 167 5.1 Introduction . 167 5.2 Method . 170 5.2.1 Mass spectrometry . 170 5.2.2 Computational chemistry . 172 5.2.3 Materials . 172 5.3 Results . 174 5.3.1 Gas phase synthesis and structural characterisation of the 4- carboxylatocyclohexyl radical anion . 174 5.3.2 Reaction of the 4-carboxylatocyclohexyl radical anion (E) with O2 184 5.3.3 Computation of the 4-carboxylatophenyl + O2 potential energy surface . 187 5.4 Conclusion . 194 6 Summary and conclusions 197 IV CONTENTS Bibliography 203 A Appendix A 235 B Appendix B 239 C Appendix C: Response to Reviewers Comments 243 LISTOF ABBREVIATIONS AC Alternating Current CAD Collision Activated Dissociation CI Chemical Ionisation CID Collision Induced Dissociation CRDS Cavity Ring-down Spectroscopy DMDS Dimethyl disulfide EI Electron Ionisation ESI Electrospray Ionisation ICR Ion Cyclotron Resonance IR Infrared LIT Linear Ion-trap MS Mass Spectrometry FT-ICR Fourier Transform Ion Cyclotron Resonance FTMS Fourier Transform Mass Spectrometry PD Photodissociation PES Photoelectron Spectroscopy PI Photoionisation PIE Photoionisation Efficiency QIT Quadrupole Ion-trap SORI-CAD Sustained Off-resonance Irradiation RF Radio Frequency UV Ultraviolet VUV Vacuum Ultraviolet v LISTOF FIGURES 1.1 Synthesis of triphenylmethyl and its peroxidation. 7 1.2 Two pathways involved in lipid peroxidation. 8 1.3 A schematic of a cavity used in CRDS. 13 1.4 Near-IR CRDS spectrum of the O-O stretching region of the methylperoxyl and phenylperoxyl radical. 14 1.5 Experimental and simulated IR spectra of the phenylperoxyl radical isolated in a 10 K argon matrix. 17 1.6 Schematic of an electron ionisation source. 18 1.7 Measurements used for calculation of resolution (¢m) and mass resolving power (m/¢m)...................................... 21 1.8 A double-focusing sector mass spectrometer. 23 1.9 A quadrupole mass analyser. 25 1.10 The flowing afterglow triple quadrupole mass spectrometer. 27 1.11 Ion cyclotron motion . 30 1.12 Cubic FT-ICR cell . 31 1.13 The hyperbolic endcaps and ring electrode of a 3D ion-trap. 32 1.14 The hyperbolic linear quadrupole ion-trap of the ThermFisher LTQ Mass Spectrometer. 32 1.15 The stability region of an ion within a linear quadrupole. 33 1.16 A stability diagram illustrating the low-mass cutoff in an ion-trap. 34 1.17 Resonance forms of the benzoyl cation. 37 1.18 Characterisation of distonoid radical cations. 38 +· . + 1.19 Comparison of CH3OH and CH2OH2 by CID. 42 1.20 CID spectrum of a) ionised ethanol and b) its ¯-distonic isomer. 44 vi LIST OF FIGURES VII 1.21 Potential energy surface of the 1-propanol radical cation and its γ-distonic counterpart. 45 1.22 (a) Comparison of reaction efficiency to IE-EA for a number of neutral reactions. (b) An ionic curve-crossing model. 57 2.1 (a) Gas phase UV absorption spectrum of iodobenzene and pentaflu- oroiodobenzene. (b) UV absorption spectra of iodocyclohexane and iodoadamantane in n-heptane. 60 2.2 Temporal variation and curvature of the m/z 172 reactant ion in the pseudo- first order decay curve obtained during reaction of tert-butyl isocyanide with the N-(3,5-dehydrophenyl)-3-fluoropyridinium ion. 61 2.3 266 nm PD spectrum for the +10 charge state of iodo-Cytochrome c demon- strating exclusive loss of iodine atom and 266 nm PD spectrum for the +10 charge state of Cytochrome c showing no fragmentation without the presence of an iodinated residue. 62 2.4 UV absorption spectrum of 2-thioxopyridin-1(2H)-yl isobutyrate in acetoni- trile. ........................................... 63 2.5 Photographs of the modified backplate of an ThermoFisher LTQ. 65 2.6 Schematic of the ThermoFisher LTQ back plate modifications. 66 2.7 Photographs of the laser instrumentation and digital PCB board modified to receive a TTL trigger. 67 2.8 Dialog windows in Xcalibur to turn on TTL trigger output . 68 2.9 Pulse sequences for laser pulse generation. 69 2.10 Exploded schematic of the ion source in a ThermoFisher LTQ Mass Spec- trometer. 70 2.11 a) Isolation and 266 nm PD of N,N,N-trimethyl-4-((2-thioxopyridin-N- yloxy)carbonyl)benzeneaminium cation. Isolation and b) 266 nm PD and c) CID of 3-iodo-N,N,N,4-tetramethylbenzeneaminium cation. Isolation and 266 nm PD of d) 4-iodomethyl-N,N,N-trimethylbenzeneaminium cation. 74 2.12 Isolation of the m/z 149 fragment ion generated by PD (266 nm) of 3-iodo- N,N,N,4-tetramethylbenzeneaminium cation in the presence of O2. 75 2.13 Isolation of the m/z 149 fragment ion generated by CID of 3-iodo-N,N,N,4- tetramethylbenzeneaminium cation in the presence of O2. 76 VIII LIST OF FIGURES 2.14 Isolation of the m/z 149 fragment ion generated PD (266 nm) of 4- iodomethyl-N,N,N-trimethylbenzeneaminium cation in the presence of O2. 77 2.15 Generation of the 3-carboxylatoadamantyl radical anion from 3-(N- oxycarbonyl-2(1H)-pyridinethione)adamantane-1-carboxylate anion . ..
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