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  • TITLE
  • DEDICATION
  • DECLARATION
  • CERTIFICATE
  • ACKNOWLEDGEMENT
  • ABSTRACT
  • PREFACE
  • CONTENTS
  • ABBREVIATIONS
  • LIST OF TABLES
  • LIST OF FIGURES
  • 1. INTRODUCTION
  • 1.1. Introduction to Organic Mass Spectrometry
  • 1.1.1. The Mass Spectrometer
  • 1.1.2. The Nature of Mass Spectra
  • 1.2. Ionization Methods in Organic Mass Spectrometry
  • 1.2.1. Introduction
  • 1.2.2. Gas-Phase Ionization
  • a. Electron Ionization (EI)
  • b. Chemical Ionization (CI)
  • 1.2.3. Particle Bombardment
  • a. Fast Atom Bombardment (FAB)
  • b. Secondary Ion Mass Spectrometry (Liquid SIMS)
  • 1.2.4. Electrospray Ionization (ESI)
  • 1.2.5. Matrix-Assisted Laser Desorption Ionization (MALDI)
  • 1.3. Mass Analysis
  • 1.3.1. Sector instruments
  • 1.3.2. Quadrupole mass analysers [1a-c]
  • 1.3.3. Time-of-Flight
  • 1.3.4. Ion Detectors
  • a. Electron Multiplier
  • b. Photo Multiplier
  • 1.4. Tandem Mass Spectrometry
  • Fig.1.2. Ion optics of a four-sector mass spectrometer
  • 1.4.1. Product ion mass spectrum:
  • 1.4.2. Precursor ion mass spectrum:
  • 1.4.3. Constant neutral mass spectrum:
  • 1.4.4. Collision Activated Dissociation (CAD) Spectrum.
  • 1.5 Basic Fragmentations of Ions in Mass spectrometry.
  • 1.5.1 Ortho effects of nitro group in mass spectrometry.
  • 1.6. Gas-Phase intramolecular Cyclisations in Mass spectrometry.
  • 1.7. References
  • 2. The Mass Spectrometry-Induced Cyclisation of ProtonatedN- (2-benzoyloxyphenyl) benzamide: A Gas-Phase Analog of a Solution Reaction
  • 2.1 Scope
  • 2.2 Results and Discussion
  • Fig 2.2.1, FAB Mass Spectrum of N- (2-benzoyloxy phenyl) benzamide (Compound 1) Peaks at m/z 219, 289 and 307 are due to matrix ions.
  • Fig 2.2.2; FAB, MI Mass Spectrum of N- (2-benzoyloxy phenyl) benzamide
  • Fig 2.2.3; FAB, CAD Mass Spectrum of N- (2-benzoyloxy phenyl) benzamide
  • Fig 2.2.4; FAB Mass Spectrum of N- (3-benzoyloxy phenyl) benzamide.The ions of m/z 136, 154, and 307 are due to matrix.
  • Fig 2.2.5; FAB, MI Mass Spectrum of N- (3-benzoyloxy phenyl) benzamide
  • Fig 2.2.6; FAB Mass Spectrum of N- (4-benzoyloxy phenyl) benzamideThe ions of m/z 136, 154, and 307 are due to matrix.
  • Fig 2.2.7; FAB-MI Mass Spectrum of N- (4-benzoyloxy phenyl) benzamide.The ion of m/z 213 is [M+H - 105]+.
  • Table 2.2.1. Partial FAB mass spectra of compounds 1-3.
  • Fig. 2.2.8. FAB CAD mass spectra of ions of m/z 196 from (a) Compound 1 and (b) Protonated 2- phenyl benzoxazole
  • Fig. 2.2.9. (a) ESI mass spectrum and (b) ESI-CAD of Compound 1
  • Fig. 2.2.9. (c) ESI-CAD HRMS of Compound 1
  • Fig. 2.2.10; The CAD spectra of m/z196 ions obtainedfrom, (a) compound 1 and (b) 2-phenylbenzoxazole, by ESI ionization
  • Fig, 2.2.11, The ESI-CAD mass spectrum ofN- (3-benzoyloxy phenyl) benzamide
  • Fig. 2.2.12. ESI-CAD mass spectrum of [M + H]+, m/z 332 fromCompound 4
  • Fig. 2.2.13, FAB MI mass spectrum of [M + H]+, m/z 332Of Compound 4
  • Table 2.2.2: The relative enthalpies (heats) of formation of various transition states, Intermediates and products relative to M1a.
  • Fig. 2.2.14. The FAB-MI mass spectrum of [M + D]+ of compound 1.
  • Fig.2.2.15. The FAB-CAD mass spectrum of [M + D]+ ofCompound 1
  • Fig. 2.2.16. The EI mass spectrum of the ortho isomer, compound 1
  • Fig. 2.2.17a. The EI-MI mass spectrum of the ortho isomer, compound 1
  • Fig. 2.2.17b; The EI-CAD mass spectrum of the ortho isomer, Compound 1
  • Fig.2.2.18; The EI mass spectrum of the meta isomer, compound 2.
  • Fig. 2.2.19; The EI-CAD mass spectrum of the meta isomer, compound 2
  • Fig. 2.2.20; The EI mass spectrum of the para isomer, compounds 3.
  • Fig. 2.2.21; The EI-CAD mass spectrum of the para isomer, Compound 3
  • Fig.2.2.22. EI-CAD mass spectra of m/z 195 from (a) Compound 1 and (b) 2- phenyl benzoxazole
  • Fig. 2.2.23, MI spectrum of the molecular radicalCation of compound 4.
  • Fig. 2.2.24: The EI-CAD mass spectrum of the molecular radical cation ofCompound 4
  • 2.3 Conclusion.
  • 2.4 Experimental Details
  • 1. Preparation of N- [2- (benzoyloxy) phenyl]-benzamide. [26]
  • 2. Preparation of N- [3- (benzoyloxy) phenyl]-benzamide. [26]
  • 3. Preparation of N- [4- (benzoyloxy) phenyl]-benzamide. [26]
  • 4. Preparation of N- [2- (benzoyloxy) phenyl]-4-methyl benzamide. [26]
  • 5. Preparation of 2-Phenyl Benzoxazole. [1]
  • 2.5 References.
  • 3. The Gas Phase Cyclisations of 2-Nitrophenyl Aryl EthersUpon Protonation: A Mass Spectrometric Study
  • 3.1. Scope
  • 3.2 Results and Discussion
  • Fig. 3.2.1. Partial FAB mass spectrum of 2-nitrophenyl phenyl ether, matrix3-nitrobenzyl alcohol. (MNBA)
  • Fig. 3.2.1a.FAB mass spectrum of 2-nitrophenyl phenyl ether, matrix 3-nitrobenzyl alcohol (The ions of m/z 136, 154 are due to the matrix)
  • Fig. 3.2.2. FAB mass spectrum of 4-nitrophenyl-phenyl ether, matrix 3-nitrobenzyl alcohol. (The ions of m/z 136, 154 are due to the matrix)
  • Fig.3.2.3, MI mass spectrum of the [M+H]+ ion of m/z 216 from2- nitrophenyl phenyl ether
  • Fig. 3.2.4, FAB- CAD mass spectrum of [M+H]+, m/z 216 of ether 1
  • Fig. 3.2.5, FAB-MI mass spectrum of the [M+H]+ ion of m/z 216 from 4- nitrophenyl phenyl ether
  • Fig.3.2.6, FAB-CAD mass spectrum of the [M+H]+ ion of m/z 216 from 4-nitrophenyl phenyl ether.
  • Fig. 3.2.7a, CAD mass spectrum of the ion of m/z 182 from N-acetyl phenoxazine
  • Fig. 3.2.7b, CAD mass spectrum of the fragment ion of m/z 182 from ether 1.
  • Scheme 3.2.3a, Proposed mechanism for formation of ions of m/z 182, 198 and 199.
  • Fig. 3.2.8. ESI mass spectrum of the molecular ion [M+H]+ ion of2-nitrophenyl phenyl ether (ether 1)
  • Fig. 3.2.9, (a) & (b) ESI-CAD mass spectrum of ether 1Plotted in two different mass ranges (Both at higher energy 10 volts) (c) ESI-CAD MS of ether 1 at low energy 7 volts
  • Table 3.2.1. ESI-CAD- HR mass spectral data of the fragment ions from ether 1
  • Scheme 3.2.3b, Proposed mechanism for the elimination of CO from the ions of m/z 198.
  • Fig. 3.2.10, CAD –MS of the collisionally produced ion of m/z 198 by MS3Experiments on ESI generated the [M+H]+ ion of ether 1
  • Scheme 3.2.4, Proposed mechanism for formation of ions of m/z 122 and 94.
  • Fig.3.2.11. FAB-CAD mass spectrum of the [M+D]+ of ether 1, m/z 217
  • Fig.3.2.12, CI mass spectrum of 2-nitrophenyl phenyl ether
  • Fig.3.2.13, CI-MI mass spectrum of 2 -Nitrophenyl phenyl ether.
  • Fig.3.2.14, CI-CAD mass spectrum of 2- Nitrophenyl phenyl ether
  • Fig. 3.2.15 CI-CAD mass spectrum of the ion of m/z 182 from [M+H]+ ion of Ether 1
  • Fig. 3.2.7a, EI-CAD mass spectrum of the ion of m/z 182 from N-acetyl phenoxazine
  • Fig.3.2.16, CI-MI mass spectrum of [M+D]+ from 2-nitrophenyl phenyl ether (Ether 1)
  • Fig.3.2.17, CI-CAD mass spectrum of [M+D]+ from 2-nitrophenylphenyl ether.
  • Fig.3.2.18. Partial FAB mass spectrum of 2-nitrophenyl-4’methyl phenyl ether, (Ether 3) matrix MNBA
  • Fig. 3.2.19. FAB mass spectrum of 2-nitrophenyl-2’methyl phenyl ether, (ether 4) Matrix MNBA
  • Fig. 3.2.20. FAB MI mass spectrum of 2-nitrophenyl-4’methyl phenyl ether
  • Fig. 3.2.21. FAB MI mass spectrum of 2-nitrophenyl-2’methyl phenyl ether
  • Fig. 3.2.22. FAB CAD mass spectrum of 2-nitrophenyl-4’methyl phenyl ether (3)
  • Fig. 3.2.23, FAB CAD mass spectrum of 2-nitrophenyl-2’methyl phenyl ether
  • Fig. 3.2.24, FAB MI mass spectrum of 4-nitrophenyl-2’methyl phenyl ether
  • Fig. 3.2.25. FAB CAD mass spectrum of 4-nitrophenyl-2’methyl phenyl ether.
  • Scheme.3.2.6: Proposed mechanism for the formation of ions of m/z 196 and 212 (Methyl group is either ortho or para)
  • Scheme 3.2.7: Proposed mechanism for the formation of ions of m/z 122 and 108.
  • Table 3.2.2: Partial FAB mass spectral data of compounds 1 to 5.
  • Table 3.2.3, Partial FAB MS/MS mass spectra of the [M + H]+ ions of ethers 1 to 5. (The figures in parenthesis denote ion abundances)
  • Fig.3.2.26, The ESI mass spectrum of 2-nitrophenyl-4’- methylphenyl ether (ether 3)
  • Fig.3.2.27. ESI-CAD-HRMS mass spectrum of the molecularion [M+H]+ of ether 3
  • Fig.3.2.28, ESI-CAD-HRMS of the molecular ion [M+H]+ of ether 3. (The masses of the ions are displayed up to four decimal places)
  • Table.3.2.4. Measured accurate masses of the fragment ions from ether 3.
  • 3.3. Conclusion
  • 3.4 Experimental Details
  • 1. Preparation of 2-Nitrophenyl phenyl ether [35]
  • 2. Preparation of 4-Nitrophenyl phenyl ether [35]
  • 3. Preparation of 2-nitrophenyl-2’-methyl phenyl ether [35]
  • 4. Preparation of 2-nitrophenyl-4’-methyl phenyl ether [35]
  • 5. Preparation of N-acetyl Phenoxazine [40]
  • 3.5. References.
  • 4. The Mass Spectrometric Investigation ofProton Induced Cyclisations of 2-nitro-N-phenyl anilinesIn Gas-Phase
  • 4.1. Scope
  • 4.2. Results and Discussion
  • Fig.4.2.1. The FAB mass spectrum of 2-nitro-N-phenyl aniline (The ion of m/z 154 is due to the matrix)
  • Fig.4.2.2, FAB-MI, mass spectrum of [M+H]+ion of m/z 215
  • Fig.4.2.3. FAB-CAD mass spectrum of [M+H]+, m/z 215
  • Fig.4.2.4a, FAB-CAD mass spectrum of the ion of m/z 197
  • Fig.4.2.5, CI- CAD mass spectrum of the ion of m/z 198
  • Scheme 4.2.2, Schematic representation of the fragmentation pathways for the [M+H]+ ionfrom compound 1.
  • Fig.4.2.6, FAB- CAD mass spectrum of the ion of m/z 181
  • Fig.4.2.7. The ESI (a) mass spectrum and (b) CADMass spectrum of 2-nitro-N-phenyl aniline
  • Table 4.2.1, Measured accurate masses of the fragment ions from the ESI-CADMass spectrum of the [M+H]+, ion of 2-nitro-N-phenyl aniline.
  • Fig. 4.2.4b, CAD –MS of the collisionally produced ion of m/z 197 by MS3Experiments on the ESI generated [M+H]+ ion of compound 1
  • Fig. 4.2.8 (a) The FAB-CAD mass spectrum of ion of m/z 180from Compound 1,
  • Fig.4.2.8 (b) The CAD mass spectrum of ion of m/z 180 fromPhenazine radical cation
  • Fig.4.2.9, The CI mass spectrum of 2-nitro-N-phenyl aniline
  • Fig.4.2.8 (b) The CAD mass spectrum of the ion of m/z 180 fromPhenazine radical cation
  • Fig.4.2.10, The CAD mass spectrum of the ion of m/z 180 fromCompound 1 by CI
  • Fig. 4.2.11 (a) CI-CAD mass spectrum of the ion of m/z 181from [phenazine + H] + (b) CI- CAD mass spectrum of the ion of m/z 181from [M+H]+ ion of compound 1
  • Scheme 4.2.4; Proposed mechanism for formation of ions in ESI and FAB ionisation.
  • Scheme 4.2.5, Proposed mechanism for formation extrusion of CO from M1 ([M+H-H2O]+)
  • Scheme 4.2.6: Proposed mechanism for the extrusion of OH from [M+H-H2O]+
  • Fig.4.2.12, The CI- MI mass spectrum of [M+D]+ ion of 2-nitro-N-phenyl aniline
  • Fig.4.2.13, The FAB- MI mass spectrum of [M+H]+ ion of4-nitro-N-phenyl aniline.
  • Fig.4.2.14, The CAD mass spectrum of [M+H]+ ion of 4-nitro-NPhenylaniline
  • Fig.4.2.15, The ESI mass spectrum of4-nitro- N-phenyl aniline
  • Fig.4.2.16, The ESI -MS/MS–HRMS of 4-nitro- N-phenyl aniline
  • Fig.4.2.17; The FAB mass spectrum of N- (4-methylphenyl) -2-nitro aniline
  • Fig. 4.2.18 (a) The ESI and (b) ESI-CAD mass spectrum of the [M+H]+ ion of compound 2
  • Table 4.2.2. Measured accurate masses of the fragment ions from the ESI-CAD massSpectrum of the [M+H]+, ion of 2-nitro-N- (4-methylphenyl) aniline.
  • Fig. 4.2.19 (a) The ESI and (b) ESI-CAD mass spectra of the [M+H]+ ion of compound 3
  • Table 4.2.3. Measured accurate masses of the fragment ions from the ESI-CADMass spectrum of the [M+H]+, ion of N- (4-chlorophenyl) 2-nitro aniline.
  • Fig. 4.2.20 (a) The ESI and (b) ESI-CAD mass spectra of the [M+H]+ ion of compound 4
  • Table 4.2.4. Measured accurate masses of the fragment ions from the ESI-CADMass spectrum of the [M+H]+, ion of Compound 4.
  • 4.3 Conclusion
  • 4.4 Experimental Details
  • 1. Preparation of N- (4-methylphenyl) -2- nitro aniline (2) [1]
  • 2. Preparation of N - (4-chloro phenyl) -2-nitroaniline (Compound 3) [1]
  • 3. Preparation of 4-chloro-N- (4-methylphenyl) -2-nitroaniline. (Compound 4) [1]
  • 4.5 References
  • 5. Intramolecular Cyclisations of2-Nitrophenyl Aryl thioethers upon ProtonationIn Mass Spectrometry
  • 5.1. Scope
  • 5.2. Results and Discussion
  • Fig. 5.2.1, The FAB MS of [M+H]+ ion of 2-nitrophenyl phenylSulphide (thioether 1)
  • Fig. 5.2.2, The FAB-MI-MS of the [M+H]+ ion of 2-nitrophenyl phenylsulphide
  • Fig. 5.2.3, The FAB-CAD mass spectrum of the [M+H]+ion of thioether 1.
  • Fig. 5.2.4, CI-MS of the [M+H]+ ion of the thioether 1
  • Fig. 5.2.5. The CI-MI mass spectrum of the [M+H]+ ionof 2-nitrophenyl phenyl sulphide.
  • Scheme 5.2.2. Schematic representation of the fragmentation pathways for the [M+H]+ ionfrom thioether 1.
  • 5.2.1. Mechanism of eliminations of H2O and two OH radicals from protonated thioether 1.
  • Scheme 5.2.3. Proposed mechanism for the eliminations of H2O and two OH radicals.
  • Fig.5.2.6 (a) CI-MI mass spectrum of the [M+D]+ion of thioether1
  • Fig.5.2.6 (b), Partial CI-CADmass spectrum of the [M+D]+ion of Thioether 1
  • Fig.5.2.7a. The FAB-CAD mass spectrum of the [M+H- H2O]+ ion ofm/z 214 from thioether 1.
  • Scheme 5.2.4. Proposed mechanism for the extrusion of CO from the ion of m/z 214
  • Fig. 5.2.7b, CAD–MS of the collisionally produced ion of m/z 214 by MS3Experiment on ESI generated [M+H]+ ion of thioether 1.
  • Fig.5.2.8, CI-CAD mass spectrum of [M+H-OH]+ ion from thioether 1.
  • Scheme 5.2.5. Proposed fragmentation processes of the ion of m/z 215 from thioether 1
  • 5.2.2. Mechanism of eliminations of SO, SO2 and SO2 H radical from protonated thioether 1.
  • Fig. 5.2.9, The CI-MI mass spectrum of the [M+H]+ ion of 2-nitrophenyl phenylSulphide of m/z 234 with 34S isotope.
  • Scheme 5.2.6. Proposed mechanism for the elimination of SO, SO2 and SO2 H radical.
  • Fig. 5.2.10 (a) FAB-CAD MS of the ion of m/z 184 from thioether 1 (b) CAD mass spectrum of the radical cation of Dibenzothiophene.
  • Scheme 5.2.7, The fragmentation pathways for the ion of m/z 184.
  • 5.2.3, ESI mass spectral study of thioether 1 upon protonation
  • Fig. 5.2.11, The ESI –MS of the [M+H]+ ion of thioether 1
  • Fig. 5.2.12. The ESI –CAD -MS of the [M+H]+ ion of thioether 1
  • Table.5.2.1, Measured accurate masses of the fragment ions from the ESI-CAD massspectrum of the [M+H]+, ion of 2-nitrophenyl phenyl sulphide (Thioether 1)
  • Fig.5.2.13. Measured accurate masses of the isobaric ions of m/z184from the ESI-CAD MS of the [M+H]+, ion of thioether 1
  • Fig. 5.2.14. The ESI mass spectrum of the [M+H]+ion of thioether 1
  • Fig. 5.2.15. The ESI –CAD mass spectrum of theion of m/z 248 from thioether 1.
  • Fig. 5.2.16. The ESI-CAD mass spectrum ofthe [M+H]+ion of sulphoxide (m/z 248)
  • Scheme 5.2.8, Mass spectral fragmentations pathways for the ion of m/z 248 onESI-CAD analysis.
  • Table.5.2.2, Measured accurate masses of the fragment ions from the ESI-CAD massspectrum of the [M+H]+, ion of m/z 248 from thioether 1.
  • 5.2.3, FAB and ESI mass spectral study of Thioethers 2-4 upon protonation.
  • Fig. 5.2.17, The FAB-MS of [M+H]+ ion of 4-nitrophenyl phenyl sulphide
  • Fig.5.2.18, The FAB –MI, MS of [M+H]+ ion of thioether 4
  • Fig.5.2.19, ESI mass spectrum of thioether 4.
  • Fig.5.2.20, ESI –CAD mass spectrum of the [M+H]+ion of thioether 4.
  • Table.5.2.3, Measured accurate masses of the fragment ions from the ESI-CAD massSpectrum of the [M+H]+ ion of thioether 4.
  • Fig. 5.2.21, ESI-CAD mass spectrum, of the ion of m/z 248 formed bythe electrochemical oxidation of the thioether 4.
  • Fig. 5.2.22, ESI- mass spectrum, of the [M+H]+ion from the thioether 2.
  • Fig. 5.2.23, ESI- CAD mass spectrum, of the [M+H] ion from the thioether 2
  • Fig. 5.2.24, ESI- CAD mass spectrum, of the ion of m/z 282
  • Table.5.2.4, Measured accurate masses of the fragment ions from the ESI-CAD massSpectrum of the ion of m/z 282 generated from thioether 2.
  • Scheme 5.2.12, ESI-CAD- MS fragmentations pathways for the ion of m/z 282.
  • Fig. 5.2.25, ESI- mass spectrum, of the [M+H] ionfrom the thioether 3
  • Fig.5.2.26, The ESI-CAD mass spectrum of the [M+H] ion fromthe thioether 3.
  • Fig. 5.2.27, ESI-CAD mass spectrum of the ion of m/z 282
  • Table.5.2.5, Measured accurate masses of the fragment ions from the ESI-CAD massSpectrum of the ion of m/z 296 generated from thioether 3
  • Scheme 5.2.14, ESI-CAD- MS fragmentations pathways for the ion of m/z 296
  • 5.3. Conclusion
  • 5.4. Experimental Details
  • 1. Preparation of 1-nitro-2- (phenylthio) benzene (thioether 1) [13].
  • 2. Preparation of 4-chloro-2-nitro-1- (phenylthio) benzene (thioether 2) [13]
  • 3. Preparation of 4-chloro-1- [ (4-methyl phenyl) sulfinyl]-2-nitrobenzene [13]. (Thioether 3)
  • 4. Preparation of 4-nitro-2- (phenylthio) benzene (thioether 4) [13].
  • 5.5 References
  • 6. Experimental -General Considerations
  • 6.1. Synthesis
  • 6.2. Mass spectrometry
  • 6.3.Theoretical Calculations
  • 6.4 References
  • SUMMARY
  • List of Publications
  • Poster Presented at Symposia
  • Contributed Papers Presented at Workshops and Symposia