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CHARACTERISATION OF REACTIONS RELEVANT TO USING MASS SPECTROMETRY

Mahendra Bhujel B.Sc (Hons I), LaTrobe

Principal Supervisor: Professor Stephen Blanksby Associate Supervisor: Professor Steven Bottle

Submitted in fulfilment of the requirements for the degree of Doctor of Philosophy

School of Chemistry, Physics and Mechanical Engineering Science and Engineering Faculty Queensland University of Technology 2017

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry i

ABSTRACT

Ozone plays a significant role in the chemistry of the lower (troposphere) and upper () atmosphere. In these regions, ozone undergoes a myriad of chemical reactions with both organic and inorganic substrates and can include reactions with ions as well as neutrals. These processes are critical for a range of atmospheric processes ranging from filtering damaging short wavelength solar radiation through to the formation of secondary organic . Detailed understanding of many of these fundamental ozonolysis reactions in the gas is often limited due to the inability to study reactions in isolation and to trap and interrogate reaction intermediates.

In this thesis, state-of-the-art ion-trap mass spectrometric techniques have been deployed to study archetype reactions of ozone with selected organic (cyclohexene carboxylic acids) and inorganic substrates (iodide and ). These experiments are accompanied by quantum chemical calculations that assist in rationalising the experimental observations. 1- and 3-cyclohexene carboxylate anions ([1-CCA-H]- and [3-CCA-H]-) were generated using negative mode ionisation. The reactions of these anions with ozone were carried out in a modified linear ion-trap mass spectrometer which was infused with ozone through an ozone-mixing manifold. The experiments were carried out under pseudo-first order conditions and the pseudo-first order rate constants were determined. The ozonolysis rates for the [1- CCA-H]- ions was determined to be 12.5 times faster than the ozonolysis rate for the [3-CCA-H]- isomer. This enhanced ozonolysis rate was rationalised as arising from substitution of the -carbon in this isomer. Charge loss processes dominated the ozonolysis reaction for both these ions. Computational predictions revealed that the ozonolysis of these ions was exothermic by 60 kcal mol-1 which is similar to the energies for their neutral counter parts.

The study of the gas phase ozonolysis reaction of I- ion was carried out using - - - the same instrumentation. In the reaction of I ion with excess ozone, IO , IO2 and - - - IO3 ions were formed. However, IO and IO2 ions were formed in low abundances. To circumvent this problem, an in-source ozonolysis technique was applied resulting - - in the formation of abundant IO and IO2 ions. Subsequently, the reaction kinetics

ii Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

for the reaction between these ions and ozone were individually probed by mass selecting the ions in the ion-trap and trapping the ions in the presence of ozone for a predetermined period of time. The formation of the IO- ion from the reaction of the - - - I ion and ozone as well as the formation of the IO2 ion from the reaction of IO and ozone was found to be reversible. In both instances, the forward oxidation step was faster than the reversible step. Also, the reaction between Br- ion and ozone was found to be intrinsically slow. High level computational studies at the UCCSD/6- - 311+G(d,p) level of theory on the singlet surface for the reaction of Br and O3 showed that the barrier for the successive 2nd and 3rd O- addition to Br- were lower than the initial addition to form BrO- ion.

Finally, the real time molecular analysis of ozone derived secondary organic was demonstrated using an aerosol generation and analysis experimental set-up. Aerosols from d-Limonene were generated and analysed in real-time using extractive electrospray. Employing an automated, data dependent routine during the acquisition of data, it was possible to obtain some aspects of chemical information in real-time via the collision-induced dissociation mass spectra of the most abundant ions. It was found that most of the low-mass products formed from the ozonolysis of d-Limonene were dominantly carboxylic acids consistent with the literature.

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry iii

TABLE OF CONTENTS

Abstract ...... ii

Table of Contents ...... iv

Statement of Original Authorship ...... xix

Acknowledgements ...... xx

Aim and Thesis overview ...... xxi

Chapter 1: Part A: Introduction to Atmospheric Chemistry ...... 23

1.1 Atmospheric Chemistry ...... 23 1.1.1 Ozone in the upper atmosphere ...... 24 1.1.2 Ozone in the lower atmosphere ...... 27

1.2 Mechanisms of Ozonolysis ...... 30

1.3 Theoretical studies of ozonolysis ...... 31

1.4 Possible role of ozonolysis products and intermediates in the atmosphere ..... 33

1.5 Ozone and its role in aerosol formation ...... 34

1.6 in the lower atmosphere ...... 38

1.7 Analysis of compounds of atmospheric relevance ...... 39

Chapter 1: Part B: Mass Spectrometry ...... 41

1.8 Mass Spectrometry: An introduction ...... 41

1.9 Ion sources ...... 41 1.9.1 Electron ionisation ...... 41 1.9.2 Chemical ionisation ...... 42 1.9.3 Electrospray ionisation (ESI) ...... 44

1.10 Mass analysers ...... 46 1.10.1 Time-of-flight (TOF) ...... 47 1.10.2 Sector instruments ...... 48 1.10.3 Quadrupole mass analysers ...... 49 1.10.4 Ion-traps ...... 50 1.10.5 Tandem mass spectrometry (MS/MS) ...... 52 1.10.6 Collision induced dissociation (CID) ...... 53

iv Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

1.10.7 Studies of reactions of ions with ozone ...... 54

Chapter 2: Method development and instrumentation ...... 55

2.1 Ion- reactions ...... 55

2.2 Instrument modification for ion-molecule reactions ...... 58 2.2.1 Normal and ion-molecule mode ...... 58 2.2.2 Layout of the ozone mixing manifold ...... 59

2.3 Ozone safety ...... 67

2.4 Measuring reaction rate ...... 68 2.4.1 Reaction efficiency ...... 69

2.5 Proof of principle ion-molecule reactions ...... 70 - 2.5.1 Reaction of I + O3 ...... 70

2.5.2 Control of O3 gas delivery ...... 72 2.5.3 Reproducibility of ozone delivery ...... 77

2.6 In-source ozonolysis ...... 78

2.7 Aerosol chemistry experiments ...... 80 2.7.1 Aerosol generation and analysis ...... 84 2.7.2 Proof of concept aerosol generation experiment ...... 87

Chapter 3: Ozonolysis of cyclohexene carboxylates ...... 89

3.1 Introduction ...... 89

3.2 Methods ...... 94 3.2.1 Materials ...... 94 3.2.2 Instrumentation ...... 95 3.2.3 Statistical analysis ...... 95 3.2.4 Computational method ...... 96

3.3 Results and Discussion ...... 97 3.3.1 Overview of the experiment ...... 97 3.3.2 Benchmarking of ozone in the ion-trap ...... 98 3.3.3 Ozonolysis of 1-CCA-H- and 3-CCA-H- ions ...... 98 3.3.4 Charge loss processes ...... 104 3.3.5 Explanation for the enhanced reaction rates ...... 102 3.3.6 Rationalisation of products observed experimentally ...... 102 3.3.7 Potential energy surface for 1- and 3-cyclohexene carboxylate and ozonolysis ...... 106

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3.3.8 TS geometries for the ozonolysis of 1-cyclohexene-1-carboxylic acid and 1-cyclohexene-1-carboxylate ...... 111

3.4 Conclusion ...... 115

Chapter 4: Reaction of iodide and bromide ions with ozone in the gas phase 117

4.1 Introduction ...... 117

4.2 Methods ...... 119 4.2.1 Instrumentation ...... 119 4.2.2 Computational method ...... 120

4.3 Results and Discussion ...... 121 4.3.1 Iodide and ozone reactions ...... 121 4.3.2 Bromide and ozone reactions ...... 129 4.3.3 Computational results ...... 130

4.4 Conclusion ...... 135

Chapter 5: Development of a charge-tagging approach for the characterisation of chemical intermediates in the formation of secondary aerosols from the ozonolysis of cyclohexenes...... 139

5.1 Introduction ...... 139

5.2 Methods ...... 141 5.2.1 Aerosol generation and filter extract analysis ...... 141

5.3 Results and discussion ...... 143 5.3.1 Identification of abundant products of limonene ozonolysis ...... 146 5.3.2 Monitoring changes to the mass spectrum profile ...... 151 5.3.3 Variability in ozone concentration and ion counts ...... 153 5.3.4 Particle number concentration ...... 154 5.3.5 Off-line filter analysis ...... 155 5.3.6 Online analysis of 1-cyclohexene carboxylic acid ozonolysis ...... 156 5.3.7 Particle concentration and variability in ozone ...... 158

5.4 Conclusion ...... 159

Chapter 6: Summary and Conclusions ...... 161

6.1 Gas phase reactions of cyclohexene carboxylate anions with ozone ...... 161

6.2 Gas phase reactions of iodide and bromide anions with ozone ...... 163

vi Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

6.3 Development of a charge-tagging approach for the characterisation of chemical intermediates in the formation of secondary aerosols from the ozonolysis of cyclohexenes 164

6.4 Future work ...... 166

Bibliography ...... 168

Appendix A ...... 183

A.1 Computational methods ...... 183

A.2 Benchmarking of computational method ...... 183

A.3 Cartesian coordinates of optimised structures ...... 193

Appendix B ...... 205

- - B.1 Kinetic plots of IO + O3 and IO2 + O3 reactions ...... 205

B.2 Cartesian coordinates of optimised structures ...... 206

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry vii

LIST OF ABBREVIATIONS

CI Criegee Intermediate

CID Collision-Induced Dissociation

EI Electron Impact Ionisation

ESI Electrospray Ionisation

LIT Linear Ion-Trap

PES Potential Energy Surface

POZ Primary

SOA Secondary Organic Aerosol

SOZ Secondary Ozonide

MS Mass Spectrometry m/z Mass-to-Charge Ratio

MSn Multiple-Stage Mass Spectrometry (in n stages)

SLPM Standard Litres per Minute

viii Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

LIST OF FIGURES

1.1: The layers of the atmosphere from the troposphere to the stratosphere………23 1.2: The original data from Farman et al. is represented by unfilled triangles which show the continual fall in total ozone at Halley, from 1956 to 1994. Subsequent data shows the continual trend. Figure from Reference 14…………….27 1.3: The role of oxidants and NO in conversion of organic compounds in the troposphere. Adapted from Reference 4…………………………………………….28 1.4: A typical potential energy diagram for the ozonolysis of drawn from a range of electronic structure calculations.25 The formation of the primary ozonide is predicted to be exothermic by more than 50 kcal mol-1. In the gas phase, this excess energy remains in the system and can fuel further transformations such as to overcome the barriers to the CI formation which can have either the syn or anti- conformers. The syn-conformer can isomerise to the vinylhydroperoxide (VHP) and the anti-conformer isomerises to the ……………………………………...29 1.5: Secondary reactions resulting from CI: a) (i) Dipolar additions giving rise to a secondary ozonide and (ii) dipolar addition of two CI to form a cyclic geminal diperoxide; b) Addition of CI to an organic acid forming AAHP; c) The formation of a peroxyhemiacetal from the reaction of AAHP with an ; d) The reaction of the peroxyhemiacetal with an acid and e) Reaction of CI with an olefin forming a ketone…………………………………………………………………………….…31 1.6: The ESI process shown for the generation of positive ions from and analyte solution. The electrospray is generated due to the potential difference between the spray needle and the plate. Oxidation takes place at the needle and reduction in the metal plate. The resulting ESI droplet successively shrinks in size resulting in in- tact gas phase ions. Figure from Reference 66…………………………………...... 46 1.7: The quadrupole mass analyser. (a) The cross section of the electrical connections of the cylindrical rods. (b) Schematic of the quadrupole mass analyser. Figure from Reference 86……………………………………………………….….50 1.8: A schematic of a linear ion-trap. Figure from Reference 84……………...52 1.9: Representation of the mass analyser during the scan out operation. Ions are guided into the ion-trap and the ion-trap scans out ions with increasing m/z values. The scanned out ions are detected by an off-axial detection system. Figure from Reference 85…………………………………………………………...... 53

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry ix

1.10: The synthesis of reagent ions from pre-selected ions in an ion-trap mass spectrometer using collision induced dissociation………………………………….54 2.1: Schematic of the modified Thermo Scientific LTQ XL linear ion-trap mass spectrometer………………………………………………………………………....61 2.2: Photograph of the ozone-mixing manifold……………………………….…62 2.3: (a) Photograph showing the gas line from the ozone mixing manifold going into the back of the mass spectrometer. The region (b) is expanded (c) showing the switching valve between the ion-molecule mode (IM) and the normal mode operation of the mass spectrometer…………………………………………………………….63 2.4: Schematic of the ozone trolley utilised in the ozonolysis experiments….…65 2.5: The ozone trolley in the laboratory. The trolley consists of an ozone generator, ozone monitor, flow adjustment valves and an ozone monitor………….66 2.6: The current layout of the ozone mixing manifold, the LTQ mass spectrometer and the ozone trolley in the laboratory……………………………………………...67 2.7: The reaction of the iodide ions with ozone in the ion-trap for a pre- determined reaction time, (a) 100 ms and (b) 1000 ms………………………….…72 2.8: (a) The normalised kinetic plot of the ozonolysis of the iodide (I-) ion. (b) The log plot of the precursor m/z 127 ion as a function of the reaction time. The linear regression fit was gives the equation of the straight line and the R2 value is also given………………………………………………………………………. ….72 2.9: Plots of the normalised ion counts against the reaction time of the decay of - - the I (m/z 127) ion and the growth of the IO3 (m/z 175) product ion using the (a) 50 mm and (b) 100 mm restriction. The mean and standard deviation for at least 50 individual scans are plotted for each reaction time………………………………….74 2.10: Comparison of the pseudo-first order rate constants of the reaction between I- and O3 when using the 50mm restriction and the 100mm restriction…………….…74 2.11: Plots of the natural logarithm of the abundance of the m/z 127 ion (normalised to the total ion count) at reaction times between 0.01 s and 10 s. Data from 3 different concentrations indicated in the plot are measured external to the ion- trap mass spectrometer……………………………………………………………....75 2.12: Plot for determination of the internal ozone concentration in the ion-trap for a given external ozone concentrated generated. The equation of the liner fit as well as the R2 value is stated. This relationship is only valid when using a long (100 mm) - restriction tube and is benchmarked for the I + O3 reaction……………………….76

x Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

2.13: Normalised ion count plots of the reaction between the iodide ion and ozone at the (a) start and (b) end of the day. Exponential functions were fitted for the m/z 127 data points and the equation of the fit and the R2 values are given……………77 2.14: The onset of discharge when employing high spray (8kV) and using gas as the nebulising gas in the ESI interface……………………….…….79 2.15: The relative abundance of the m/z 125 iodide ion and the ozonolysis product m/z 175 ion as a function of spray ………………………………………….80 2.16: The experimental set-up for the 1-CCA pick-up experiment consisting of a + gas source, a flow-meter, a beaker and a retort-stand holding the N2 vapour line into the ESI interface. ……………………………………………………….…82

2.17: Individual spectra obtained during (a) Blank, (b) N2 flow On and (c) N2 flow off conditions of the experiment…………………………………………………….83 2.18: (-) ion TIC for the m/z range 124.5-125.5. The dotted lines show the onset of the switch in N2 flows during the experiment. Switching the N2 flow on results in the appearance results in the increase in ion signal arising from the appearance of m/z

125 ions in the spectra shown in Figure 2.15(b). Switching the N2 flow off causes the ion signals counts to diminish…………………………………………………...….84 2.19: The schematic of the online aerosol generation and analysis experimental set- up………………………………………………………………………………….... 85 2.20: The installation of the aerosol line guide on the side of the ESI inlet. The front panel is open to show the aerosol flow line protruding out of the aerosol line guide. The aerosol flow line is inserted into the aerosol line guide and is sealed with Teflon tape to prevent outflow of gas from the ESI source…………………………86 2.21: The profile changes before the addition of d-Limonene to the reaction bottle and after the addition. Successful generation and ionisation of aerosol compounds are indicated by the presence of three major clusters of peaks……………………….…87 3.1: Structures of endocyclic alkenes: a) α-Pinene, b) Limonene c) Cyclohexene and d) Cyclohex-1-ene-1-carboxylate anion……………………………………...…89 3.2: Some gas phase products identified from the ozonolysis of cyclohexene. Gas phase products from Reference 122 & 123…………………………………………90 3.2: Overview of ion-molecule reaction stages between ozone and pre-selected ions in the ion-trap mass spectrometer. Different scan-out stages in the ion-trap are labelled as MSn. The corresponding representative spectrums are also given. (a)

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Represents the full-MS scan, (b) represents the isolation scan for the mass-selected isolated ion and (c) represents product-ion scan following entrapment of ions in the presence of ozone for a given amount of time (1.5 s in this example) showing the appearance of new peaks………………………………………………………….97 3.4: Mass spectra of the ozonolysis of 1- and 3-CCA-H- ions, m/z 125, as a function of reaction time between the mass ranges of m/z 50 to 200. Only the spectra resulting from a reaction time of 1, 4 and 9 seconds for each species are shown for comparison…………………………………………………………………………99 3.5: Data points resulting from reaction time of 0.3 to 5 seconds are fitted using a single-term exponential function for both 1- and 3-CCA-H- ion ozonolysis. The error bars represents standard deviation of the data points for at least 50 acquired scans………………………………………………………………………………100 3.6: The potential energy surface depicting the energetics of charge loss process outlined in Scheme 3.2…………………………………………………………….103 - 3.7: Zero-point corrected PES for the O3 – 1-CCA (neutral, black) and 1-CCA-H (charged, red) reaction (syn pathway for Criegee mechanism) calculated at the B3LYP/6-31+G(d,p) level of theory. The prefix D and C represents DeMore and the Criegee pathways with D1 and C1 representing the reaction pathway for the neutral 1-CCA and ozone reaction and D2 and C2 representing reaction pathway for the 1- CCA-H- and ozone reaction. PreC, TS, Prod and SOZ refer to the pre-reactive complex, transition state, products and secondary ozonide respectively…………107 - 3.8: Zero-point corrected PES for the O3 – 3-CCA (neutral, black) and 3-CCA-H (charged, red) reaction (syn pathway for Criegee mechanism) calculated at the B3LYP/6-31+G(d,p) level of theory. The prefix D and C represents DeMore and the Criegee pathways with D3 and C3 representing the reaction pathway for the neutral 3-CCA and ozone reaction and D3 and C3 representing reaction pathway the 3-CCA- H- and ozone reaction. PreC, TS Prod and SOZ refers to the pre-reactive complex, transition state, products and secondary ozonide respectively…………………….109 3.9: TS geometry for ozone-neutral (1-CCA) and ozone-ion(1-CCA-H-) complex for the Criegee (a,b) and the DeMore (c,d) mechanisms…………………………..110 3.10: TS geometry for ozone-neutral (1-CCA) and ozone-ion (1-CCA-H-) complex for the Criegee (a,b) and the DeMore (c,d) mechanisms………………………...... 111 3.11: The isomeric structures of the epoxide and the β-lactone………………….112 3.12: The PES of propenoate ion ozonolysis. The formation of the epoxide and β-

xii Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

lactone from the POZ is shown separately to highlight the different processes…...113 4.1: Negative mode MS spectra of KI solution: a) Full negative MS spectrum of methanolic solution of KI; b) 30 ms isolation of the m/z 127 ions in the ion-trap, the region between m/z 135 – 165 is magnified 50x to show the absence of any ions c) 10 s isolation of the m/z 127 ions in the ion-trap in the presence of ozone resulting in the formation of m/z 175 ions………………………………………………………….119 4.2: Photo-dissociation spectrum of the isolated m/z 175 peak produced in - reaction between I and O3 within the ion-trap…………………………………….120 - - 4.3: Kinetics of the I and O3 reaction. (a) The exponential decay of the I ion - counts is matched by the corresponding rise in the IO3 peaks. (b) Linear fit of the pseudo first order reaction. The equation of the fit as well as the R2 value is given. The error bars represent 1σ of at least 50 different data points at the reaction time.121 4.4: The residual plot showing the deviations between the predicted and observed - data points in the linear fit of I + O3 reaction as given in Figure 4.3(b)………….121 - - 4.5: Reaction of in-source produced IO and IO2 ions with ozone for 90 ms: (a) - - Reaction of the m/z 143 ion (IO ); (b) Reaction of the m/z 159 ion (IO2 ) with ozone for 90 ms………………………………………………………………………. ….123 - - 4.6: Kinetics of the reactions between O3 and IO (a) and IO2 (b) in the ion- trap………………………………………………………………………………....124 - - 4.7: Reaction of in-source produced IO and IO2 ions with oxygen in the ion-trap - - for 5 s: a) Reaction of the m/z 143 ion (IO ); b) Reaction of the m/z 159 ion (IO2 ) …………………………………………………………………………………….125 - 4.8: Reaction of in-source produced IO3 ions with oxygen in the ion-trap for 5 s…………………………………………………………………………………….126 4.9: Production of m/z 79 ions and its subsequent reaction with ozone: a) The CID spectrum of m/z 213 ion resulting in the formation of the ion amongst other CID products; b) Ions at m/z 95, 113 and 127 were formed when 79Br- was trapped with O3 for 10 s…………………………………………………………………… 127 - 4.10: The singlet transition state structures for the reaction between BrO and O3 - (left) and BrO2 and O3 (right). Interatomic distances in angstroms and bond angles are given…………………………………………………………………………... 129 - - 4.11: The intrinsic reaction coordinate (IRC) pathways for the BrO (left) and BrO2 (right) reaction with ozone obtained at the UMP2 level of theory……………..….130

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry xiii

- - 4.12: The potential energy surfaces for the BrO + O3 (top) and BrO2 + O3 (bottom) reactions at the UCCSD\6-311+G(d,p) level of theory. Only the starting products, the transition state and the final products are shown. All species are in the singlet state and the energies are relative to the starting products for the reactions. The energies are reported in kJ mol-1…………………………………………….131 5.2: Panel (a) shows the installed aerosol line guide from the side of the ESI source. Panels (b) and (c) shows the side view of the ESI source showing the changes to its configuration before and after the installation of the aerosol line guide. Panel (d) and (e) shows the Schott bottle cap with the attached Swagelok fittings as well as the sample introduction hole………………………………………………………136 5.3: EESI (-) mass spectrum (a) before and (b) after the injection of limonene into the Schott bottle. The pictures correspond to different stages of the experiment before and after the addition of limonene in the presence of ozone in the bottle. Spectrum (b) also indicates three regions colour coded according to the groups of masses: Group 1 in blue (50 < m/z < 300), Group II in beige (300 < m/z < 450) and Group III in green (450 < m/z < 600). The mass range 450 – 1000 is magnified 10x to highlight the presence of Group III peaks……………………………………………………139 5.4: EESI (-) mass spectrum (a) before and (b) after the injection of limonene in the Schott bottle in the presence of ozone. Only the mass range m/z 50-300 is shown to highlight the Group 1 peaks……………………………………………………. 140 5.5: Anions of limonoic acid (1) and 7-hydroxy-limonaldehyde (2) have been detected in the (-) mass spectrometric analysis of limonene ozonolysis samples. 5.6: Panels a – f shows the mass spectrum of the CID (MS2) fragments of the precursor ions shown. Certain areas are magnified to highlight ions with low abundances…………………………………………………………………………141 5.7: The (-) ion TIC trace for the limonene ozonolysis experiment in given in panel (a). Panels b – f shows the integrated mass spectrum across the TIC for the duration of each experimental stage which is colour coded. Panel (g) shows the O2 blank spectrum prior to the introduction of ozone in the reaction chamber……… 142 5.8: The variation of ozone concentration (a) and the particle concentration (b) overlayed on top of the total ion chromatograph trace for the limonene ozonolysis experiment………………………………………………………………………….144 5.9: A filter was sampled for 10 mins with ozone passing through in the absence of limonene ozonolysis particles at the start of the experiments and another filter

xiv Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

paper was sampled with the limonene ozonolysis particles during the second stage of the limonene ozonolysis experiments. The resulting (-) ESI mass spectrums of the extracts of these filters are given. Panel (a) is the mass spectrum for the filter blank extract and panel (b) is the mass spectrum for the filter aerosol extract…………...145 5.10: Panel (a) shows the (-) ion TIC for the 1-CCA ozonolysis experiment. Panels b – d shows the integrated EESI mass spectrum for the colour coded regions in the

TIC. Panel (f) shows the EESI blank mass spectrum obtained while having only O2 in the reaction chamber………………………………………………………….…151 5.11: The variation of ozone concentration (a) and the particle concentration (b) overlayed on top of the total ion chromatograph trace for the 1-CCA ozonolysis experiment…………………………………………………………………………153

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry xv

LIST OF SCHEMES

1.1: ozonolysis. The production of the diradical Criegee intermediate which can either be stabilised or decompose either to a dioxirane, a carboxylic acid or a vinyl hydroperoxide……………………………………………………………30 2.1: The differentiation between the epoxide functionality from isomeric ketones and carbonyl ylide using ion-molecule reactions between epoxide cations and . Scheme adapted from Reference 7………………………………….…56 3.1: The first steps of ozonolysis of cyclohexene via the Criegee and DeMore mechanism. The reactants, transition state of the cycloaddition (TSCG) and the product, primary ozonide (POZ) is shown for the Criegee mechanism. DeMore mechanism highlights two transition states, exo-TSDM and endo-TSDM with the resulting products, epoxide and molecular oxygen and primary ozonide (POZ) respectively. The decomposition pathways (a) and (b) of the POZ results in the formation of compounds CI1 and CI2 which can participate in other reactions. CI1 and CI2 can undergo 1,3-dipolar cycloaddition to form secondary (SOZ).93 3.2: An example of a charge loss process starting from a primary ozonide……....102 3.3: Suggested reaction mechanism for the formation of the m/z 139 and m/z 60 ion during the ozonolysis of the 1-CCA-H- ion…………………………………….…105 3.4: Formation of a (a) β-lactone from the primary ozonide derived from the ozonolysis of propenoate ion. (b) Charge induced formation of an epoxide from an α- lactone also derived from the primary ozonide from the propenoate ion and ozone reaction…………………………………………………………………………….112 4.1: The forward and reversible reactions with the representative reaction rate constants for the reaction between containing ions with ozone and oxygen in the gas-phase……………………………………………………………………….126 5.1: Scheme depicting the ozonolysis of limonene and the production of Criegee intermediate products (CI1 and CI2) and secondary ozonide. The Criegee intermediate products can undergo rearrangement reactions to yield the suggested m/z 183 products……………………………………………………………...……144 6.1: The production of m/z 60 ion from the ozonolysis of 1-cyclohexene carboxylate ion……………………………………………………………………………….…156 6.2: The sequential oxidation steps of the iodide ion with ozone……………….…158

xvi Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry xvii

LIST OF TABLES

3.1: Rate constants measured for the ozonolysis of 1 & 3-CCA in the modified ion-trap mass spectrometer……………………………………….…………….…101 4.1 Geometric parameters for the species at singlet and triplet surfaces calculated at the UCCSD/6-311+G(d,p) level of theory.……………………….……………128

xviiiCharacterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

STATEMENT OF ORIGINAL AUTHORSHIP

The work contained in this thesis has not been previously submitted to meet requirements for an award at this or any other higher education institution. To the best of my knowledge and belief, the thesis contains no material previously published or written by another person except where due reference is made.

Signature: QUT Verified Signature

Date: April 2017

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry xix

ACKNOWLEDGEMENTS

This dissertation would not have been possible without the involvement and support of many people. Ultimately, I would not have been on this path without the encouragement of my joint supervisors during my honours year, Dr Evan Robertson at LaTrobe University and Dr Melita Keywood from CMAR, CSIRO. Although it seems like a long time ago, thank you for introducing me to the fascinating world of research.

I would like to thank my principal supervisor Professor Stephen Blanksby for always being there for me through the ups and downs during my time both at the University of Wollongong and here at QUT. Your guidance as a leader is inspiring and thank you for always being patient with me.

Also, my sincere thanks goes to friends I have made at UOW during my time there. Thank you, Marty, Monica, Tom and Matt for helping me to adjust to both the research and the university lifestyle. I would also like to thank Assistant Professors Stephen Wilson and Adam Trevitt for their feedback and assistance in my research at UOW. I wish all the UOW folk all the best for the future.

At QUT, I am thankful to the current mass group. Thank you, Dave, Peggy and Berwyck for your endearing support and guidance in the laboratory. It was always nice to have someone around to be able to ask about something I didn’t know. I am looking forward to working with you guys again the future.

Finally, I will like to thank my family, friends and counsellors both in QUT and externally for helping me see through my PhD years. Some days were incredibly difficult but I feel emboldened and richer through your effort and time invested in me. Alas, thank you mum and dad for believing in the beauty of my dreams from day one.

xx Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

Aim and Thesis overview

In this thesis, ozonolysis reactions in the gas and particle phase will be explored. The objectives of this thesis are: 1. Construction of an ozone-mixing manifold to facilitate the controlled introduction of laboratory generated ozone into an ion-trap mass spectrometer 2. The modification of a commercially available mass spectrometer to allow the introduction of ozone into the ion-trap region of the mass spectrometer 3. Characterisation of atmospherically relevant ozonolysis reactions in the gas phase using the current state-of-the-art techniques and the modified ion-trap mass spectrometer 4. Rationalisation of the experiments using quantum chemical calculation 5. Characterisation of ozonolysis reaction in the particle phase by constructing an aerosol generation set-up and subsequent analysis of particle phase ozonolysis products using extractive electrospray

The body of this thesis is presented in four distinct parts:

Chapter 1 (Part A) provides an overview of the importance of understanding ozone chemistry in both the upper and lower atmosphere. The current understanding of the reactions of ozone with organic and inorganic compounds present in the atmosphere is discussed. The importance of the reaction between volatile organic compounds with ozone is also outlined.

Chapter 1 (Part B) introduces mass spectrometry as the main instrumental technique used in the research as described in this dissertation. This section covers a brief history of mass spectrometry with a focus on important parts of the instrument. An overview of the commercial mass spectrometer used in this research is also presented to provide the reader with an understanding of the conventional functions of the instrument upon which customization, as a part of this research, have afforded unique capabilities.

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry xxi

Chapter 2 is a dedicated method developments chapter. Modifications to the commercial mass spectrometry instrument to enable ion molecule reactions are detailed. Data analysis methods are also presented in this chapter.

Chapter 3 - 5 discusses the results from the three main topics of research carried out for the PhD project. Chapter 3: The reaction of 1- & 3-cyclohexene carboxylates with ozone, Chapter 4: The reaction of Iodide and Bromide ions with ozone and Chapter 5: The real-time analysis of externally generated aerosol using electrospray-ionisation mass spectrometry.

Chapter 6 is a conclusion chapter and provides a general discussion of the research presented in this dissertation as well as the practical and theoretical significance.

xxii Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

Chapter 1: Part A: Introduction to Atmospheric Chemistry

1.1 Atmospheric Chemistry

Atmospheric chemistry is concerned with the atomic and molecular composition of the atmosphere surrounding the and how chemical reactions modulate composition throughout the different layers of the atmosphere. For the purposes of this project, the atmosphere is defined as the region closest to the Earth, the troposphere (< 10-15 km) through the tropopause (~10-15 km), to the stratosphere (~10-50 km) (Figure 1.1).

Figure 1.1: The layers of the atmosphere from the troposphere to the stratosphere.

The Earth’s surface is suffused with a myriad of chemicals, and a wide range of physical and chemical processes govern the concentrations of these chemicals in the atmosphere. For instance, the emission, , lifetimes and fates of certain anthropogenic (man-made) and biogenic (natural) chemicals are examples of such

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 23

processes.1 These processes sometimes exert influence across the atmosphere, from the troposphere to the stratosphere. These processes and the chemistry are interconnected. Homogeneous and heterogeneous reactions occur throughout the atmosphere and certain reactions can have important consequences both locally (e.g., episodes in polluted regions) and on a global scale2 (e.g., affecting the which is the difference of sunlight absorbed by the Earth and energy radiated back to space).

In this chapter, the current understanding of the many roles of ozone in the atmosphere is presented, with a particular focus on reaction of ozone with neutrals and ions in the different layers of the atmosphere.

1.1.1 Ozone in the upper atmosphere

In the stratosphere, the is critical for the modulation of solar radiation reaching the surface of the Earth. At this part of the atmosphere, ozone concentrations can reach as high as 12 ppm. It provides a blanket of protection from the damaging UV radiation as well as initiating other key stratospheric chemical reactions.3 The flux of short wavelength radiation (λ < 315 nm) into the troposphere is limited as a result of the concentration of ozone in the stratosphere. Thus, within the stratosphere, increasing are associated with increasing temperatures as a result of this absorption of solar radiation.

Stratospheric chemistry is dominated by the photolysis of O3 as indicated in Equations (1.1);

+ ℎ ( < 315 ) →( ) + ( ∆) (1.1)

The production of the electronically excited oxygen initiates the free chemistry of the stratosphere, through reactions with , and nitrous for instance. The can intrude into the troposphere and react with water producing hydroxyl radicals.4

Stratospheric ozone is usually recorded as total ozone integrated throughout the Earth’s atmospheric column and is measured in Dobson units (DU). One Dobson

24 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

unit is the height of a layer of pure ozone gas in units of 10-5 m if all the atmospheric ozone was isolated and compressed to a layer at 1 atm and 273 K.1 Thus 200 DU is equivalent to the pure ozone thickness of 1 mm. Generally, ozone columns increase with latitude especially in winter and spring, with the O3 production rate being highest around the equatorial belt. Ozone concentrations in the atmosphere are thought to be maintained at a steady state by the set of reactions shown in Equations (1.2-1.5) that are known as the Chapman cycle5;

+ℎ ( < 242 ) →2 (1.2)

+ → (1.3)

+ → 2 (1.4)

+ℎ ( ≤ 336 ) →( ) + (1.5)

The bond dissociation energy of dioxygen is 118 kcal mol-1 and corresponds to a threshold wavelength of 242 nm for .6 The oxygen atom produced in reaction 1.2 can be excited O(1S) or O(1D) or ground state O(3P) atoms depending on which is produced at the given threshold wavelength. The ozone consuming reactions 1.4 and 1.5 serves to counter-balance the over production of ozone. In the 1960s, the rates for these reactions were well established, and it was apparent that the reactions represented by the cycle were higher than the observed levels of stratospheric ozone.7 Thus it was suggested that another loss mechanism for ozone must be operative. This loss mechanism was unravelled and involves as indicated in Equations (1.6-1.10).8 Subsequently, the reactions of these of nitrogen with ozone were the key “missing links” in determining stratospheric ozone concentrations. These reactions constitute a catalytic cycle because the NO used up in reaction 1.8 is replaced in reaction 1.10.

+ℎ → +( ) (1.6)

→+() (1.7)

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 25

+ → + (1.8)

+ →+ (1.9)

+ℎ →+ (1.10)

Chlorofluorocarbons (CFCs), such as CF2Cl2, have long lifetimes in the troposphere; this is due to a variety of reasons.9 They do not absorb light of wavelength above 290 nm and do not react significantly with O3, OH or NO3. Furthermore, they are not readily soluble in water and thus are not removed rapidly via wash out.1 As a result, CFCs are transported across the tropopause to the stratosphere (Figure 1.1).10 With increasing altitudes, the CFCs eventually get exposed to wavelengths between 185-210 nm that result in photodissociation to atomic , which reacts with ozone as illustrated in Equations 1.11-1.12.11

+ ℎ ( < 240 ) → + (1.11)

+ → + (1.12)

+ → + (1.13)

Following photoactivation at wavelengths < 240 nm, the weaker C-Cl bond (76 kcal mol-1 for C-Cl vs 110 kcal mol-1 C-F) breaks and the released Cl atom reacts in a catalytic chain that to the destruction of O3. From various studies, it is now understood that rather than gas phase reactions of CFCs with ozone, heterogeneous chemistry on polar stratospheric clouds plays an important role for observed ozone 1 losses. In this processes, atomic chlorine reservoir species such as HCl and ClONO2 12 react rapidly on ice surfaces generating Cl2 and HNO3. Once released, the gaseous chlorine undergoes rapid photolysis to form atomic chlorine which then proceeds to destroy ozone via reaction 1.12 and 1.13.

26 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

The catalytic cycle involving chlorine and ozone was not discovered until 1973 by Molina and Rowland and not until 1985 did Farman, Gardiner, and Shanklin report loss of large amounts of ozone over Halley Bay, Antarctica (Figure 1.2).11,13

Figure 1.2: The original data from Farman et al. is represented by unfilled triangles which show the continual fall in total ozone at Halley, Antarctica from 1956 to 1994. Subsequent data shows the continual trend.14

As a result of their predictions and insightful work on the catalysed destruction of ozone in the stratosphere, Paul J. Crutzen, Mario J. Molina, and F. Sherwood Rowland were awarded the Nobel prize in Chemistry in 1995.

1.1.2 Ozone in the lower atmosphere

Volatile organic compounds (VOCs) released in the troposphere have both biogenic and anthropogenic sources. These VOCs in the presence of trace atmospheric oxidants such as the (OH), radical (NO3) or 1 ozone (O3) undergo chemical transformation. Such reactions can result in products of low vapour pressure (lower volatility) that can partition between the vapour and phases by either condensing on pre-existing particles or forming a critical nucleus upon which other gases can condense.14 The first oxidation steps to an array of compounds which generally include polar oxygenated functional groups such as , ketones, alcohols, , , carboxylic acids,

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 27

hydroperoxides and percarboxylic acids among others.15 Furthermore, subsequent oxidation can take place and this form of chemical evolution can take place in either the gas or the particle phase. Given the importance of the interactions between VOCs and oxidants in the troposphere, the investigation of these reactions and ozone in particular has been of significant interest.

Approximately 90% of the ozone present in the atmosphere is found in the stratosphere and only 10% is in the troposphere; ozone concentrations in the troposphere (typically 0.04 ppm) are much lower than in the stratosphere (typically 12 ppm).1 However the photolysis of ozone followed by the reaction with water provides a primary source of hydroxyl radicals, which is the main oxidant in the atmosphere (Reaction 1.13).16,17 Ozone is also an important in the upper troposphere. Ozone in the troposphere is thought to be formed from the 18 photolysis of NO2 (Reaction1.14). Although a fraction of total NO2 emitted into the troposphere is via processes, most of it is formed by the oxidation of NO which has natural, biogenic and industrial sources. This conversion of NO to NO2 is part of larger processes where oxidation of organic compounds is initiated by reactants such as the hydroxyl radical.19

( ) + → 2 (1.13)

+ ℎ ( ≤ 420 ) → +( ) (1.14)

( ) + → (1.15)

In addition to the mechanisms for formation discussed already, stratospheric ozone sometimes intrudes into the tropospheric layer, providing an extra source of .10

28 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

Figure 1.3: The role of oxidants and NO in conversion of organic compounds in the troposphere.4

As shown in Figure 1.3, the hydroxyl radical abstracts from the forming an alkyl radical, which is subsequently oxidized into an alkylperoxy radical. In environments where there are high concentrations of NOx (i.e. concentrations of NO + NO2), the alkylperoxy radical reacts with NO forming an alkoxy radical and NO2. The NO2 then forms O3 (Reactions 1.14 and 1.15). In clean environments where NO is not present in considerable amounts, self-reactions of

HO2 and its reactions with RO2 and O3 becomes important. The reaction of HO2 with

RO2 and O3 becomes competitive with the reaction of NO. Therefore, whether O3 is 4 formed from VOC-NOx reactions in air depends critically on the NO concentration. It has been consistently shown that simultaneous emissions of NOx and reactive hydrocarbons in the summertime results in the efficient production of O3 downwind.20

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 29

1.2 Mechanisms of Ozonolysis

Sources of olefins in the troposphere are biogenic and anthropogenic. Terpenes are a class of olefins which are produced by plants and emitted into the troposphere. The characteristic blue seen in forested areas are thought to be due to formation of nanoparticles from the chemical processing of terpenes. The first studies of ozonolysis of olefins in the solution phase were conducted in the early 20th century.21-22 Despite many decades of research, the mechanisms of ozone-alkene reactions in the gas phase are still not well understood, certainly not as well understood as the corresponding reactions in the solution phase. The initial step of ozonolysis involves the addition of O3 across the double bond to form a primary ozonide. Due to the instability of the primary ozonide, one of the two oxygen-oxygen bonds cleaves along with the carbon-carbon bond present from the initial olefin yielding an aldehyde or a ketone and a carbonyloxide intermediate; often called the “Criegee” intermediate (CI) (Scheme 1.1).

30 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

Scheme 1.1: Alkene ozonolysis. The production of the diradical Criegee intermediate which can either be stabilised or decompose either to a dioxirane, a carboxylic acid or a vinyl hydroperoxide.

The Criegee intermediate is thought to be a zwitterion in the solution phase while in the gas phase it is usually represented as a biradical.23 The Criegee intermediate is initially excited and is either stabilized or rearranges into more stable isomeric forms such as the dioxirane, carboxylic acids or vinyl hydroperoxides as illustrated in Scheme 1. In the solution phase, the aldehyde or ketone that is formed can be trapped with the Criegee intermediate within a solvent cage. This facilitates recombination to form a secondary ozonide as indicated in Equation (1.16). Such recombination processes are less probable in the gas phase, where reaction intermediates, once formed, can be separated by large distances. Furthermore, there is a quenching of the excess energy of the excited Criegee intermediate within the solvent in the liquid phase but in the gas phase there is an inherent lack of mechanisms for the rapid removal of excess energy.24 This can have the consequence that the Criegee intermediate itself can undergo further unimolecular or bimolecular reactions as stated in the next section.

(1.16)

1.3 Theoretical studies of ozonolysis

Changes in the potential energy along the reaction coordinate for a typical ozonolysis reaction obtained from computational studies is shown in Figure 1.4.

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 31

Figure 1.4: A typical potential energy diagram representative of results from several different electronic structure methods.25 The formation of the primary ozonide is predicted to be exothermic by more than 50 kcal mol-1. In the gas phase, this excess energy remains in the system and can fuel further transformations such as to overcome the barriers to the CI formation, which can have either the syn or anti- conformers. The syn-conformer can isomerise to the vinylhydroperoxide (VHP) and the anti-conformer isomerises to the dioxirane.

In addition to the elucidation of the major pathways of the ozonolysis reactions, theory has revealed other intriguing possibilities for the formation of the CI from systems other than ozone and alkenes. Subsequent reactions of the CI with other compounds have also been investigated computationally.

The self-reactions of the CI in the gas phase obtained from the reaction of

CH2I and O2 was found to be extremely rapid (Equations 1.17 to 1.19). Quantum- chemical calculations revealed that a cyclic dimeric intermediate where the terminal O of CHOO from one CI is bonded to the carbon atom of the other CI and is formed with large exothermicity (-92 kcal mol-1).25 Such self-reactions have previously been overlooked and provide an explanation as to why the measured lifetimes of CHOO differed between groups.26

32 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

+ → + (1.17)

+ → 2 + ( ∆) (1.18)

→ () (1.19)

Computational investigations have also suggested that the CI can combine with ozone itself yielding an interesting 5 membered ring consisting of five oxygen -1 27 atoms (H2CO5) (~-47 kcal mol ). Ultimately, the compound dissociates into and . This would serve to ultimately reduce the concentration of the ozone if this was the dominant pathway for the CI loss in the atmosphere and thus also reduce the concentration of OH radicals in the atmosphere. However, the reaction rate is yet to be determined.

1.4 Possible role of ozonolysis products and intermediates in the atmosphere

One of the biggest challenges in tropospheric chemistry in recent times has been to elucidate the nature of unknown pathways or chemistry which produces OH radicals. Forests are known to have clean atmospheres with low NOx concentrations. Experiments done in Finnish forests shown that the OH yields are higher than expected in the absence of NOx and therefore the existence of this other compound was suggested which introduces another source of OH radicals besides the reactions of ozone and monoterpenes during evenings and nights.28 Ozone photolysis provides an important source of OH radicals but is inefficient during those periods. Clearly the presence of monoterpenes enhanced the OH radical generation. As such it was thought that the culprit might well be CI produced during the ozonolysis of these monoterpenes and preliminary solution phase and matrix isolation studies have determined the CI to be efficient oxidants capable of forming OH radicals.29

Current knowledge of the gas phase chemistry of ozonolysis and Criegee intermediates has been steadily expanded under laboratory conditions via what can be termed as classical kinetic methods.30 Usually, CI scavengers are utilized to determine the concentration of these reactive species. In such cases, it is assumed that only the stabilized forms of the CI participate in these scavenging reactions

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 33

while the energised CI decomposes or rearranges. Given the propensity of the CI to rearrange it is challenging to assign subsequent trapping or other reactions exclusively to the reactive intermediate and not to the isomeric vinyl hydroperoxide or dioxirane isomers.

To overcome this issue, synchrotron photoionisation has been employed as a sensitive method to selectively probe CI chemistry.31 One attractive facet of such a technique is that it allows the distinction between isomers based on their photoionization spectra. However, during ozone-alkene reactions the slow reactions of ozonolysis and relatively fast reaction of CI results in low concentration of CI. In such a case, simply detecting the presence of the CI may not be sufficient and other systems must be looked at.

Taatjes et al., successfully detected the first CI in the gas phase using synchrotron photoionisation mass spectrometry for the gas phase oxidation of DMSO by O2. This reaction was initially suggested as a possible source of CI using computational methods.32 The reaction between the methylsulfinic methyl radicals and oxygen results in the formation of alkyl peroxy radicals and subsequent dissociation produces the CI and a methylsulfinyl radical.

Another approach relies on the reaction between O2 and α-iodoalkyl radicals to form the CI.33 In this case, the CI yields are sufficient to make certain educated inferences regarding the kinetics of the reactions of CI and atmospherically relevant compounds. For instance, it was found that the reactions between CI and SO2 occur at a substantially faster rate than previously estimated (4 orders of magnitude faster).This is important because this may potentially contribute to the formation of

H2SO4, which has been shown in experiments to influence atmospheric aerosol production.34 In contrast, the reaction of the CI with NO was found to be surprisingly slow (a factor of 100 smaller than previous estimates) and the reaction with NO2 was faster than anticipated.

1.5 Ozone and its role in aerosol formation

Globally, the emissions of biogenic organic compounds by plants dwarf anthropogenic emissions. Monoterpenes (C10H18) represent an important class of

34 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

organic compounds which represent about 10% of the total biogenic hydrocarbon emissions.17 They consist of two units which can be cyclic or acylic. The cyclic compounds can have endo or exogenic double bonds. In the atmosphere, these compounds are oxidised by OH and NO3 radicals and O3. While reactions with OH dominate, reactions with O3 form many low volatility products which can condense onto existing particles and contribute to SOA formation.

In the laboratory, particle phase monoterpene ozonolysis is studied using spherical vessel reactors, flow reactors and mixing chambers where ozone and the species are reacted for a finite time and the products either analysed on-line or off-line using various methods which incorporate sample collection methods.17 Methods such as gas chromatography-mass spectrometry (GC/MS) and liquid chromatography-mass spectrometry (LC/MS) are traditional off-line methods for analysis. For GC/MS analysis, more often than not, the samples are derivatized to detect organic acids. In certain experiments, particle counters and sizers are used to investigate the changes in particle physics as a result of the uptake of ozone by the 35,36 particles where aerosol seed particles such as MgSO4 or (NH4)2SO4 are utilized. For unseeded experiments, those particle counters and sizers are employed to determine the particle counts and sizes for the new particle formation as a result of the ozonolysis. The current limitation is that the smallest diameter of particles that can be counted is 1 nm.37 While gas phase studies of monoterpene ozonolysis suggests that the reaction produces new particles, the full chemical composition of such new particles are still not well known. The primary compounds that act as the initial seeds still elude identification and the subsequent growth of these particles, which in most cases is attributed to oligomer formation is still poorly understood.

More complex and less volatile organic compounds are also known to contribute to oxidative processes in the troposphere. Although experimental evidence is less clear, fatty acids (FA) are thought to contribute significantly to the total organic fraction in the troposphere.38 There are both anthropogenic and biogenic sources of fatty acids. Cooking and gas and diesel powered exhaust are the major sources of anthropogenic FA and direct forest emissions are a significant source of biogenic FA.39 Studies by Zhao et al., determined that cooking aerosols in Guangzhou, China, consisted of 73-85% of quantifiable particulate in

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 35

40 PM2.5 (i.e., particles less than 2.5 µm in diameter). In 2010, it was reported that in Hong Kong, FA were the major component (46-80% by weight) of extractable 41 organic compounds in PM2.5 of ambient aerosols . Huang et al., reported seasonal -3 average concentration of FA at 260-483 ng m in PM2.5 where unsaturated FA being present at a lower concentration than saturated FA in , China.42

When fatty acids are being transported by aerosol there is an opportunity for their reaction with tropospheric ozone. This heterogeneous chemistry could potentially occur at the gas-particle interface or, when ozone diffuses into the particle, within the condensed phase.43 The ozonolysis of oleic acid has been regarded as a useful model system for studying the heterogeneous ozone chemistry of the troposphere. In such studies, flow tubes have had their surfaces coated by oleic acid with ozone then allowed to diffuse though the reactor. Ozone uptake is usually - - monitored by the loss of the O3 , which is formed via chemical ionisation with SF6 .44 Product studies from these flow tube reactions find that common primary products of heterogeneous ozonolysis of oleic acids are azeliac acid, nonanal, nonanoic acid and 9-oxononanoic acids. These compounds have been observed in several independent studies.43

Primary products are associated with the cleavage of one of the O-O bonds in the primary ozonide and the C-C bonds on the FA. Secondary products are usually attributed to the reactions of CI in the solution phase as shown in Figure 1.5.43 For instance, CI can react with aldehydes undergoing dipolar cycloadditions forming secondary ozonide and also self-react forming germinal diperoxides.45 Furthermore, these CI can react with carboxylic acids forming α-acyloxyalkyl hydroperoxides (AAHP).46 These compounds are thought to be polymerization propagators and responsible for high molecular weight products present in samples analysed by mass spectrometry.47

36 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

a) Dipolar Cycloadditions

H O O i) O O R' R'' O R R' R'' R O H

ii) R H R H O O OO O O H R' H R' O O

b) Addition to an acid +CI'' R O OH H O H O O O HO R' O -H O R R' 2 O O acyloxyalkyl hydroperoxide (AAHP) R O R'

c) Addition of AAHP to an aldehyde R'' OH O R O OH O R H O H R' O O O H R'' O peroxyhemiacetal R'

d) Reaction of a peroxyhemiacetal with an acid

R'' OH R'' O R''' O O O R H R H O O O R' O O HO R''' R' O O

e) Ketone/Aldehyde formation O O O H H H O R' H R CH2R' RH2C R' R R' R'' O Figure 1.5: Secondary reactions resulting from CI: a) (i) Dipolar additions giving rise to a secondary ozonide and (ii) dipolar addition of two CI to form a cyclic geminal diperoxide; b) Addition of CI to an organic acid forming AAHP; c) The formation of a peroxyhemiacetal from the reaction of AAHP with an aldehyde; d) The reaction of the peroxyhemiacetal with an acid and e) Reaction of CI with an olefin forming a ketone and two distinct aldehydes.

It has been suggested that in the troposphere rich with mono and di-acids, α- AAHP compounds may be favoured over the secondary ozonides, where the CI preferentially reacts with the acids rather than the aldehydes.48 These peroxides made up 68% of the total aerosol product mass in one particular study while the primary products 9-oxononanoic acid and azelaic acid made up only 28 and 4%

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 37

respectively.50

1.6 Halogens in the lower atmosphere

Dihalogen compounds absorb in the visible to near-UV region of the electromagnetic spectrum. The photolysis of a dihalogen produces two radicals which are highly reactive and can undergo several competing reactions such as oxygen abstraction from ozone and hydrogen atom abstraction from a hydrocarbon as shown in Equations 1.20 and 1.21 respectively where X represents a halogen species.

·+ → · + (1.20)

·+ →·+ (1.21)

The reaction of the halogen radical with a hydrocarbon (reaction 1.21) depends on the relative bond strength of the halogenated hydrocarbon, from HF through to HI. Iodine atoms are the least reactive with hydrocarbons as they react with ozone preferentially followed by bromine and to a much lesser extent, chlorine atoms which preferentially react with hydrocarbons in the troposphere.

Halogen oxides, BrO and IO derived from reaction 1.20, are subject to rapid photodissociation on seconds to minutes timescale. These oxides can participate in self-reactions as well as reactions with other halogen oxides. Reaction of halogen oxides with HO2 results in the formation of a reservoir species, HOX (Reactions 1.22);

· + · → + (1.22)

Such compounds can readily photolyse to yield a hydroxyl and a halide radical. HOX can also participate in heterogeneous reactions with halide ions which are present on condensed surfaces such as on aerosol particles and snow/ice interfaces (Reaction 1.23).

38 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

+ () → + () (1.23)

+ + () +ℎ →2+ () (Net) (1.24)

The net reaction 1.24 shows that two radicals of X are formed from a single radical. This results in the accretion of reactive halogen radicals and in the case of bromine, such events observed in ice/snow interfaces are termed as ‘Bromine explosion’ events.

Sea water is rich in halide ions with the relative abundance being chloride > bromide > iodide. Recently, interfacial chemistry involving halide ions and ozone has been observed in sea water. For instance, the presence of iodide ions on the sea water surface is thought to enhance ozone uptake resulting in the production of I2 which is degassed from the water surface. The same process is thought to occur for the discovery of enhanced Br2 gas in snow pack interface. Furthermore, this interfacial heterogeneous chemistry is also thought to occur in the surface of aerosols as it has been found that I- concentrations in sea aerosols are enhanced on by 2-4 orders of magnitude relative to the sea water concentrations.49

1.7 Analysis of compounds of atmospheric relevance

Certain compounds found in the atmosphere for analysis can either be synthesized in the laboratory or sampled from a relevant environment. For atmospheric sampling the complex array of compounds found in the atmosphere demands an arsenal of analytical instrumentation and associated methodologies. This chemical complexity was highlighted in 2007 by Goldstein and Galbally who showed that for C10 alkenes, there are about 100 possible isomers. If all the typical 50 heteroatoms are included, this value rises to over 1 million C10 isomers. Traditionally, the analysis of such convoluted systems generally incorporated off-line methods and recently, on-line methods have revolutionised atmospheric chemical analysis.

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 39

Off-line analysis generally involves large sampling size and the subsequent analysis takes a few days. Often a sophisticated and powerful technique involving a chromatographic and mass spectrometric technique is applied. They are termed as hyphenated techniques and include LC-MS (liquid chromatography, mass spectrometry) and GC-MS (gas chromatography, mass spectrometry). For instance, GC-MS is routinely used to separate, identify and quantify species within an aerosol sample. LC-MS has been applied to characterise polar fractions in aerosol obtained from laboratory chamber studies of aerosols.

On-line analysis reduces sample contamination, sample losses as well as secondary chemical reactions occurring on the collected samples. On-line mass spectrometry techniques provide some degree of chemical characterisation as well as provide near-real time information. On-line analysis of aerosols derived from isoprene oxidation revealed the chemistry involving two key reaction intermediates during isoprene ozonolysis under high and low NOx conditions.

Certain important compounds in the atmosphere cannot be isolated from atmospheric sampling for instance, transient reaction intermediates. These, often short lived, intermediates while not readily identifiable or isolated, can play important roles in influencing a range of atmospheric chemical processes. Criegee Intermediates as described in section 1.1.5 are such examples. Such intermediates are usually synthesized in the laboratory and their reactivity with a host of atmospherically relevant compounds determined from gas phase studies.

Analysis of compounds as described in this dissertation involves both on-line and off-line methods using a modified mass spectrometer. Furthermore, gas-phase ions are synthesised in the mass spectrometer to understand the reaction kinetics and product distribution of certain ion-molecule reactions.

40 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

Chapter 1: Part B: Mass Spectrometry

1.8 Mass Spectrometry: An introduction

In its simplest form, a mass spectrometer consists of an ion source, a mass analyser and a detector which are operated under high vacuum conditions. The ion source is used to volatilise and ionise the analyte of interest, the mass analyser to discriminate between different ion masses and the detector to detect the distinguished ions. A plethora of configurations of coupled ion sources and mass analysers are possible depending on experimental aims and requirements. Also, each configuration has its own advantages and disadvantages. In the following section, the theory and the technology of the implementations of the essential components of the mass spectrometer are described with regards to the production, isolation and analysis of ions in the gas phase.

1.9 Ion sources

Gas phase ions from a , liquid or a gas sample are generated in an ion source. There are different processes of ionisation such as the ionisation of a neutral molecule through electron ejection, electron capture, , deprotonation, adduct formation or the transfer of a charged species from the condensed phase to the gas phase.

1.9.1 Electron ionisation

In 1918, A. J. Dempster described electron ionization as a method to generate positive and negative ions.51 He used electrons which were generated at 128 to bombard phosphate on a piece of aluminium foil. The design was subsequently improved by Bleakney and Nier.52,53 In a contemporary electron ionisation source, a heated cathodic filament emits electrons which are accelerated towards an through a potential difference of 70 eV. Analyte gases and samples are introduced at the source and less volatile samples are sublimed under vacuum. The resulting neutral molecule M interacts with the energetic electrons as outlined in Equation 1.25.

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 41

+ →• +2 (1.25)

The electron beam interacts with the gaseous molecule resulting in an expulsion of an electron. 10 eV of energy is required to ionise most organic compounds and since a typical EI process utilises 70 eV, the additional energy imparted on the analyte molecule results in extensive fragmentation.54 The fragmentation can occur through a unimolecular dissociation generating a molecular ion, a radical ion and a neutral product and or via homolytic cleavage to form a closed shell fragment ion and a neutral radical. Despite the pervasive fragmentation produced during EI, the fragmentations are reproducible and thus provide a structural fingerprint which is ideal for structural elucidation of unknown analytes.

1.9.2 Chemical ionisation

For structural elucidation, the determination of the molecular mass of an analyte is vital. While EI provides reliable diagnostic fragmentation, at times, the molecular ion may be absent thus precluding structural elucidation. Chemical ionisation is a “soft” ionisation method which produces ions with little excess energy. This results in a mass spectrum with less fragmentation and relatively easily identifiable molecular species.

Chemical ionisation occurs as a result of the interaction between neutral gaseous and ions. Thus, in contrast to EI, bimolecular processes are utilised to yield analyte ions. The requirement of these processes is that there must be a sufficiently high number of ion-molecule collisions and in chemical ionisation, this prerequisite is fulfilled by increasing the partial pressure of the reagent gas.

In a typical chemical ionisation experiment, a reagent gas is introduced as an ionisation source at pressure of about 102 Pa.55,56 Since the background pressure of the instrument is at about 10-4 to 10-3 Pa, ionisation of the reagent gas occurs through electron ionisation. The resulting ions will then interact with other reagent gas molecules forming ionisation through a series of cascading chemical reactions. A pathway in chemical ionisation which generates a positive ion, M+H+

42 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

from the interaction between a compound, M and an acidic compound, BH is given in Equation 1.26.

+[] → [+] + (1.26)

Chemical ionisation resulting in proton transfer is the most common ionisation process. A basic molecule’s tendency to accept a proton is quantitatively described by its proton affinity (PA)57;

+ → []; −∆ =() (1.27)

The PA is () = −∆( ) − ∆( ) − ∆(). In cases where protonation is the primary experimental goal when utilizing chemical ionisation as an ionisation technique, the PAs of the analyte and the complementary base B of the proton-donating reaction ion [BH]+ (Bronsted acid) have to be considered.

Exothermic processes will result in protonation, for instance if PA(B) < PA(M). However, impurities having a higher PA than the neutral reagent gas results in the preferential protonation of the impurity. For instance, under chemical ionisation + 58 conditions, mixtures of CH4/H2O results in abundant m/z 17 ions, [H3O] .

Attachment of the ion to an analyte can also result in ion formation for + instance the presence of [M+NH4] ions observed when using as a reagent gas. Anion abstractions such as hydride abstraction is another class of ionisation process in CI; aliphatic alcohols yield abundant [M-H]- ions rather than [M+H]+ ions during CI. Lastly, charge exchange results in the formation of near thermal (low internal energy) ions.

While the production of positive ions is common, the production of negative ions requires that the neutral analyte has an acidic group or an electronegative element in the structure. This requirement allows a degree of selectivity for detection of such analyte in a mixture of compounds. In the ionisation plasma produced in chemical ionisation, low-energy electrons are ubiquitous.59 They are either produced

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 43

directly from the filament or subsequently deactivated through collisions or are formed from ionization cascade reactions. Interactions of these electrons with neutral molecules result in negative ion production via different mechanisms (Equations 1.32 – 1.34)54;

+ → • +2 (1.32)

+ → • + (1.33)

+ → + + (1.34)

1.9.3 Electrospray ionisation (ESI)

The 1970s and 80s saw the dramatic developments in the field of mass spectrometry where the solution phase was directly coupled to a mass analyser. Methods such as atmospheric pressure ionisation (API), thermospray and electrodynamic ionisation were described and applied to the ionisation of analytes in the solution phase.60–62 These techniques allowed the generation of ions at atmospheric pressure (760 Torr), used very little concentration of analyte in the solution phase (10-6 – 10-3 M) and was suited to the analysis of large, complex and non-volatile samples.

Electrospray ionisation is another API technique and its development predates the other ionisation technique mentioned above.63 However, it was only in the 1980s that Fenn and co-workers designed and described an advanced form of the ESI source.64 J.B. Fenn was awarded a third of the Nobel prize in Chemistry in 2002 and his Noble lecture was entitled “Electrospray wings for Molecular Elephants”. The title gives a sense of the challenges faced by researchers prior to the invention of the ESI; getting ions from large molecules was inherently difficult and the method provided a sense of liberation from the analytical constrains of the time. Today, it is the most commonly employed ionisation method together with matrix-assisted laser desorption ionisation and it has allowed for the unprecedented applications of mass spectrometry in chemistry and biochemistry.65,66 ESI is the ionisation method used in this dissertation.

44 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

ESI is a “soft” ionising technique and it involves the generation of analyte ions from an analyte dissolved in a solvent in the presence of an electric field (Figure 1-6). The term “soft” implies that during the ionisation process, minimum internal energy is imparted to the analyte. The analyte solution is nebulised and subsequent desolvation takes place as the analyte droplet evaporates through its journey in the charged space. The gas phase ions are generated under atmospheric pressure. ESI is one of the most utilized ionisation methods which have resulted in unprecedented biological and chemical applications of mass spectrometry.

Figure 1.6: The ESI process shown for the generation of positive ions from and analyte solution. The electrospray is generated due to the potential difference between the spray needle and the metal plate. Oxidation takes place at the needle and reduction in the metal plate. The resulting ESI droplet successively shrinks in size resulting in in-tact gas phase ions.67

During ESI, the analyte containing solution is nebulised from a spray tip driven by the applied voltage. The spray tip is held at a potential difference (i.e., 2-6 kV) with respect to the rest of the instrument. The production of charged aerosol droplets is followed by its desolvation. A counter stream of nitrogen gas aids in the evaporation of the solvent resulting in an increase in charge on the droplets. The resulting unstable droplet then overcomes its surface tension forming progeny droplets. Subsequent shrinkage and droplet disintegration results in the formation of

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 45

intact gas phase ions. These ions then pass through a sampling skimmer cone and through various pumping stages in the mass spectrometry with progressively decreasing pressure for subsequent analysis of m/z and measurement of ion abundance.

1.10 Mass analysers

Once the gas phase ions are generated, they are directed into a mass analyser. The primary role of the mass analyser is the separation of ions according to their m/z. Achieving good mass resolution, attaining high transmission efficiencies and having higher upper mass limits are important when evaluating the usefulness of the mass analyser in different applications.68

The resolving power of an instrument is the ability to differentiate between two distinct signals for ions with a small mass difference. Resolution in mass spectrometry is usually defined as the ratio of a particular mass, mi , to the difference in mass, ∆m, for two neighbouring masses (Equation 1.35).69 The difference in mass is given by the width of a peak at a specific fraction of the maximum peak height. IUPAC recommends the use of 50%, 5% or 0.5% as the fraction of the maximum peak height.70 = (1.35) ∆

As methods of volatilising molecules with larger m/z ratios became more prevalent, the need for a mass spectrometer to analyse higher masses became important. The upper mass limits determine the highest m/z value that can be detected by the instrument.

Transmission efficiency is the ratio of the number of ions entering the mass analyser and the sum of the ions reaching the detector. When using low concentrations of analyte, it is important to have high transmission efficiencies. Higher transmission efficiencies result in the acquisition of data at higher resolutions and with enhanced sensitivities.

46 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

The principle of using electric and/or magnetic fields to manipulate ion trajectory forms the heart of the technology behind mass analysers. Scanning mass analysers utilize electromagnetic fields to separate the masses according to the m/z ratios from a mixture of ions having different masses and relative abundances. During scanning, certain ions with particular masses are allowed to pass through the analyser. Scanning mass analysers includes magnetic sector and quadrupoles. Trapping mass analysers on the other hand operate by containing ions and manipulating their trajectories by using radio frequency electric fields. Trapping mass analysers are categorised as either dynamic or static traps and examples include 3-D quadrupole ion-traps and ion cyclotron mass spectrometers, respectively.

1.10.1 Time-of-flight (TOF)

A time-of-flight (TOF) analyser discriminates between different m/z ratio of ions by measuring the time taken by these ions to pass through a field-free drift path of a known length. Introduction of ions into the TOF analyser occurs in packets of ions so that the ions start at the same time as it traverses though the drift tube at a potential, Vs. An ion with mass, m, and total charge q = ze has the kinetic energy

(Ekinetic) as stated by equation 1.36.

= = = (1.36)

= (1.37)

= (1.38)

The time, t, needed to drift through the distance, d, is given in equation 1.37. Substitution of v into from equation 1.37 into equation 1.36 gives the equation 1.38. Given a constant potential and the drift tube length, it shows that the m/z ratio can be obtained by determining the value of t2. Also, the equation shows that ions with larger m/z ratios arrive at the detector at later time compared to smaller ions provided they started their flight in the drift tube at the same time.

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 47

TOF analysers have virtually no upper mass limits and they have been used to analyse large intact proteins. Furthermore, the transmittance in a TOF analyser is about 90% because unlike the scanning-type analyser where ion losses during scanning are a part of the design of the analyser, almost all of the ions introduced to the drift region of the TOF analyser will reach the detector. Mass resolution in TOF analysers can be enhanced by increasing the length of the flight tube and its sensitivity can be enhanced by increasing the acceleration voltage.

1.10.2 Sector instruments

When an ion enters a constant magnetic field, it experiences a Lorentz force,

FL, which is dependent on the velocity of the ion, v, the magnetic field strength, B, as well as the charge of the ion, q. The Lorentz force is given by,

= (1.39)

The equation is true if both the velocity and the magnetic field are perpendicular to each other. This force, FL, which is exerted on the moving charge, is perpendicular to both the velocity of the charge and the magnetic field. Thus, the natural tendency of the ion is to move in circular orbits under these conditions. During circular motion, the magnetic field provides the centripetal force which is in equilibrium with the Lorentz force,

== (1.40)

Rearranging equation 1.40 gives the radius of the circular orbit, rm,

= (1.41)

The equation shows that ions with a particular charge and momentum follow a unique circular path of radius, rm. Given that the radius, rm, is fixed obtaining a mass spectrum demands a scanning capability by varying the magnetic field to analyse different masses. An important assumption in the operation of magnetic

48 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

sector instruments is that the ions entering the magnetic field have the same entrance velocity. As such, ions with different m/z ratios can acquire identical momentum and this result in reduced sensitivity and resolution. Combining an electric sector with the magnetic sector to obtain a so-called double focusing analyser improves the resolution. In this configuration, the energy of the ions is resolved prior to entering the magnetic sector where mass separation takes place. Double focusing has helped in improving the resolution of the magnetic sector instrument by more than ten times.71–73

1.10.3 Quadrupole mass analysers

A quadrupole mass analyser consists of four perfectly parallel cylindrical or hyperbolically shaped rods assembled in a square configuration (Figure 1.7). Opposite pairs of rods are held at the same potential, either positive or negative, with both a direct current (DC) and an alternating current (AC) component (Equation 1.42).

Figure 1.7: The quadrupole mass analyser. (a) The cross section of the electrical connections of the cylindrical rods. (b) Schematic of the quadrupole mass analyser.74

Ions are introduced into the quadruple analyser in the z-direction. As the ions traverse the centre of the quadrupole it experiences an attractive force from a rod which has an opposite charge to the ions ionic charge. As the ion approaches the rod, the voltage is periodically reversed to the opposite polarity which repels the ions to the centre of the quadrupole. This sequence of attraction and repulsion in both the x-

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 49

and y- directions causes the ions to float through the quadrupole with limited amplitudes. For a given set of AC (Vcos) and DC voltages (Ucos), only ions of certain m/z ratios pass through the mass filter and all other ions are thrown off their original path.

=+cos (1.42) = − = (1.43) = − = (1.44)

The theory of the Mathieu equations describes the motion of the ion through a quadrupole (Equation 1.43 and 1.44). Given sets of values for U, V and ω, the Mathieu equations can have two different solutions, stable and unstable motions. Either the ions oscillate in the x-z plane with limited amplitudes and pass through the mass analyser in the z-direction or the oscillation amplitudes grows exponentially until the particle crashes into one of the quadrupoles and is lost. The plot of a against q yields the stability diagram of a two-dimensional quadruple field. Quadrupole mass analysers operate at unit resolution constraining their applications.73

1.10.4 Ion-traps

Ions traps are generally classified as either a linear ion-trap (LIT) or a 3-D ion-trap. End-capping the quadrupoles with higher potentials at the front and back ends creates a trapping potential within the multipoles which allows for the storage of ions. Such an ion-trap is called a linear ion-trap (LIT) (Figure 1.8).

50 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

Figure 1.8: A schematic of a linear ion-trap.75

The ThermoFisher Scientific LTQ XL 2-D linear ion-trap mass spectrometer is the mass spectrometer used in the research reported in this dissertation. In a typical MS application, gas phase ions are generated using ESI in either the positive or negative mode. The analyte solution is transferred to the ionization source with the help of an automated syringe pump on the instrument.

Gas phase ions once generated at the ion source are fed into an ion transfer tube and subsequently pass through a skimmer. The skimmer acts as a baffle between regions of different pressure; high pressure in the front interface region and lower pressure where the RF lenses are located behind the skimmer. The ions then pass through three ion optics and transmitting devices before led through to the mass analyser.

The mass analyser is a 2-D ion-trap where ion storage, isolation, collision- induced dissociation (CID) and ion ejection occurs. Helium is used as a damping and as a collision gas. When an ion beam enters the ion-trap, collision with He atoms reduces the kinetic energy of the ions. This reduced translational motion allows for greater efficiency in trapping the ions. The mass spectrometer has an off-axis detection system made up of two electron multipliers and conversion dynode.

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 51

Figure 1.9: Representation of the mass analyser during the scan out operation. Ions are guided into the ion-trap and the ion-trap scans out ions with increasing m/z values. The scanned out ions are detected by an off-axial detection system.76

1.10.5 Tandem mass spectrometry (MS/MS)

Ions of a particular mass can be selected in one mass analyser and subjected to further mass spectrometric analysis in another mass analyser. Technologies which achieve this successive mass analysis are referred to as tandem mass spectrometry (MS/MS). This is critical since the determination of an ion’s molecular mass alone is insufficient for structural elucidation and even an instrument which can measure highly accurate mass cannot distinguish between isomers.

Sequential mass analysis requires that mass changes take place. Such changes can be due to spontaneous dissociation during the manipulation of ion trajectory by electric and magnetic fields as in the case for metastable ions or such changes can arise from deliberately activating the ion. The resulting fragments are analysed to assist in the structural identification of the initially isolated ion (a precursor ion). Novel compounds can be synthesized this way.

MS/MS experiments are achieved either tandem-in-space or tandem-in-time. Mass analysers which transmit beams of ions can be placed in combination to

52 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

achieve ion discrimination over space. Trapping devices placed in tandem can used to conduct tandem-in-time experiments.

Typically, tandem MS/MS experiments in beam type analyser involve scanning through the mass range and isolating a precursor ion with the first mass analyser and using a second mass analyser to acquire a spectrum. In trapping analyser, precursor ion selection, activation and analysis occurs in the same place. The different mass stages are denoted by MSn (n ≥ 2).

1.10.6 Collision induced dissociation (CID)

CID involves the introduction of preselected ions into a collision cell where they are activated and undergo collision with inert collisional gas such as He, Ar or air (Figure 1.10). The resulting product ions can yield important structural information about reaction pathways and structural information for compound elucidation. Therefore, CID provides a powerful analytical tool and is of greater utility to the researcher than knowing the molecular mass alone.

Figure 1.10: The synthesis of reagent ions from pre-selected ions in a ion-trap mass spectrometer using collision-induced dissociation.

The collision cell is located in between mass analysers for beam type instruments. As the ion beam enters the collision cell, collision between the ions and the neutral gases results in the production of product ions. In a trapping instrument, the collision is induced by applying a resonant excitation AC voltage. This imparts

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 53

kinetic energy to the trapped ions resulting in collision with the collision gas. Successive collision causes the transfer of translational energy into internal energy.

+ →∗ +→ ++ (1.45)

Collision of such ions with neutrals takes place in the order of 10-5 s, however, ion activation occurs on the milliseconds timescale. As a result, many collisions take place such that the internal energy is overcome and molecular fragmentation occurs (Equation 1.45).

1.10.7 Studies of reactions of ions with ozone

Williams et al. used a selected ion flow tube (SIFT) instrument to explore negative ion chemistry of the reactions of ions with ozone.77 Ions were generated using an electron impact ion source and the ions were directed into a quadrupole mass filter where the ion of interest was selected. The selected ions were then injected using a helium carrier gas into a flow tube where reactant gases were also introduced. The ions and the reagent gas were allowed to react over a known distance in the flow tube. Another quadrupole mass filter resolved the reactants and products. Although they were able to determine the 2nd order rate constants for the reaction between a range of ions and ozone, there were some limitations in their study. For instance, the reaction time was limited to 2 ms and products resulting from slower reactions would not have been detected. Furthermore, electron impact is a harsh method of ionisation. The rate constants measured were in the range of 10-9 – 10-12 cm3 s-1.

In another study, Mendes et al. used a pentaquadrupole to study the reactions of ozone and positive ions.78 It consisted of three quadrupoles for mass analysis and two quadrupoles which functioned as a ion-focusing reaction chamber. The ions were generated using electron impact and maximum yields of product ions from ion molecule reactions were obtained only after 1-2 hours of continuous flow of gas mixtures.

54 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

In the next section, ion-molecule reactions are discussed in greater detail and examples of relevant instrument modifications applied to study such reactions are given. Some of the limitations stated above are also addressed.

Chapter 2: Method development and instrumentation

2.1 Ion-molecule reactions

100 years ago, experiments carried out by Dempster suggested that the origin + of the mass-to-charge (m/z ) ratio of 3 resulted from the reaction between the H2 ion + 79 and H2 to form H3 . This was one of the first reports of a gas-phase ion-molecule reaction. 50 years later Munson and Field described the application of such ion- molecule reactions to the detection of analytes; a process known as chemical ionisation.55 This softer ionization method, an alternative to electron ionisation, typically involves proton transfer ion-molecule reactions to produce diagnostic [M+H]+ ions. For instance, proton transfer from a donor ion (e.g. hydronium ion, + + H3O ) to an analyte gas, M, generates the diagnostic [M+H] ion (Reaction 2.1).

+ →[+] + (2.1)

In the previous decade alone, more than 1000 have been published with ion-molecule reactions at the heart of the research. Not only are gas-phase ion- molecule reactions fast and efficient, only small quantities of the reagent are required for the reaction. Proton transfer reactions remain the most common ionization method for volatile organic compound analysis.80 More recently, specific implementations of such ion-molecule reactions have gained traction, for differentiating isomeric compounds or functional group identification. For example, + the structural isomers of C2H5O correspond to either the protonated (1), protonated epoxide (2) or the methoxymethyl cation (3) (Scheme 1). Beauchamp and co-workers in 1973 used ion-molecule reactions to show that the epoxide cation

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 55

(1) selectively reacts with phosphine (or the protonated phosphine with the neutral epoxide) to yield a cyclic phosphonium ion which corresponds to m/z 61.81

Scheme 2.1: The differentiation between the epoxide functionality from isomeric ketones and carbonyl ylide using ion-molecule reactions between epoxide cations and phosphine. Scheme adapted from ref. 7.

Ion-molecule reactions almost always involve the inclusion of neutral reagents in the mass spectrometer. While chemical ionisation produces ions at the source of the mass spectrometer, it is a necessity to be able to mass select a particular ion to observe ion-molecule chemistry.

While many custom-built mass spectrometers allow for the addition of neutral reagents within the ion-trap, commercially built mass spectrometers need to be modified for use in ion-molecule reaction studies. For instance, in 1991, McLuckley, Glish and Van Berkel introduced the reagent 1,6-diaminohexane via an installed leak valve into a Finnigan ion-trap mass spectrometer.82 The modification allowed the reagent to effuse into the ion-trap and react with peptide fragment ions which were mass selected and isolated within the ion-trap. The ionic contents of the ion-trap were then scanned out enabling observation of the evolution of the ion- molecule reaction as a function of time. The ion-molecule reaction between the reagent and peptide fragment ions resulted in the removal of a single proton from the ions which allowed the authors to determine the charge state for the peptide fragment ions (Reaction 2.2).

56 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

(2.2)

More recent modifications to a ThermoScientific LCQ 3-D ion-trap were carried out by the Gronert group.83 The modification involved the construction of a gas mixing manifold that allowed the introduction of reagent gases to the flow of helium buffer gas without any modifications to the vacuum manifold encasing the ion-trap. Similar modifications have since been carried out by the O’Hair group at the University of Melbourne, Australia.84 The modification allowed the study of catalytic oxidation of to involving a binuclear dimolybdate - center [Mo2O6(OCHR2)] . It was discovered that out of the other group 6 elements employed in the experiments, only the compound incorporating the molybdate was critical in the catalytic conversion.

Blanksby and Harman were among the first to modify the next generation of linear ion-trap (LIT) mass spectrometers.85 The LIT is estimated to have a 15X higher ion capacity and an increased ion injection capacity compared to a 3-D ion- trap.75 These improvements resulted in increased sensitivity of the instrument. This could then be exploited for multistage experiments where the reagent ion was first prepared by one or more activation, mass-selection cycles.

Kenttamaa and co-workers used a similar strategy for observing ion-molecule reactions on LIT spectrometers.86 Furthermore, they have incorporated a laser- induced acoustic desorption (LIAD) probe for the desorption and subsequent ionisation by atmospheric pressure chemical ionisation (APCI) of non-volatile hydrocarbons which were previously not amenable to ionisation by ESI.87 They have also added an automated gas manifold for rapid switching between reagents.88 This allowed the inclusion of a maximum of three different reagents into the ion-trap for rapid, sequential ion-molecule reactions.

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 57

As a part of this PhD research program at QUT, modifications of a LIT mass spectrometer (LTQ, ThermoFischer Scientific) were carried out based on previously published accounts using similar platforms.

2.2 Instrument modification for ion-molecule reactions

Diagnostic reactions between isolated ions and neutral reagents can be observed by the addition of neutral reagents into the ion storage region of the mass spectrometer. This can be utilised to probe reaction kinetics as well as to aid in structural elucidation of the newly synthesized product within the ion-trap. The observation of ion-molecule reactions with ozone was a key motivation. Prior work by Thomas et al., showed that by introducing pre-generated ozone into the He supply via a plastic syringe enabled ion-molecule reactions between ozone and mass selected lipid ions.89 More recently, online ozone generation and delivery into a triple quadrupole geometry instrument was demonstrated.90 Thus, we wanted to implement the online generation and stable delivery into another platform, the LTQ.

Modifications were made to a ThermoFisher Scientific LTQ XL™ Linear Ion-trap Mass Spectrometer (ThermoFisher Scientific, USA) to enable the introduction of reagent gases into the helium buffer gas utilised by the mass spectrometer. This enables the introduction of the helium gas and the helium gas and reagent gas mixture via two modes of operation; the normal and ion-molecule operation conditions. The schematic shown in Figure 2.1 depicts the overview of the modification made to the instrument as well as the layout and the construction of the ozone mixing manifold.

2.2.1 Normal and ion-molecule mode

At the back end of the instrument as shown in Figure 2.1 and 2.3, a 3-way switching valve (V3) enables two modes of operation, the normal mode and ion- molecule mode. The helium flows on these two modes are both supplied by a single cylinder of UHP helium regulated to 40 PSI. In the normal operating mode, the regulated helium flow is introduced directly from the cylinder through a flow splitter,

58 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

(FLS) maintaining a pressure of ~2.5 mTorr within the ion-trap. The helium flow splitter regulates the flow of the gas (~1 mL min-1) into the mass analyser cavity of the mass spectrometer. Therefore, setting the 3-way valve to normal mode position (Figure 2.3) delivers helium to the ion-trap as intended by the manufacturer. When switched to ion-molecule mode, this supply is shut off and helium is delivered via the mixing manifold as described below. The helium flow when operating in the ion- molecule mode is controlled by the variable leak valve (VDL) and is adjusted such that the typical working pressure inside the ion-trap is ~2.5mTorr, equal to that obtained under the operating conditions of the normal mode.

2.2.2 Layout of the ozone mixing manifold

From Figure 2.1, the flow of Ultra High Purity (UHP) helium (H, Helium 5.0,

Coregas, Australia) is split via a union tee (T1, Part No. ()SS-200-3, Swagelok, Australia). 1/4 in. SS tubing directs part of the pressure regulated flow (40 ± 10 PSI) into the back of the mass spectrometer and the other part of the flow is introduced into the manifold. At the manifold, the pressure is regulated to 5 PSI

(R2, Part No. KCP1EFA2D2P20000, Swagelok, Australia) and the resulting pressure is read off a pressure gauge (PG, Part No. PGI-50M-BG60-CAQX-ABH, Swagelok, Australia).

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 59

LTQ XL linear ion-trap mass spectrometer spectrometer LTQ XL linear ion-trap mass Schematic of the modified Thermo Scientific Thermo of the modified Schematic Figure 2.1:

60 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

Photograph of the ozone-mixing manifold manifold Photograph of the ozone-mixing Figure 2.2:

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 61

Figure 2.3: (a) Photograph showing the gas line from the ozone mixing manifold going into the back of the mass spectrometer. The region (b) is expanded (c) showing the switching valve between the ion-molecule mode (IM) and the normal mode operation of the mass spectrometer.

62 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

A shut-off valve (S1, Part No. SS-42GS4, Swagelok, Australia) is connected in between the pressure gauge and the septum port (SP, Part No. SS-4-UT-A-4, Swagelok, Australia) which is linked to the manifold via another union tee (Part No.

SS-200-3, Swagelok, Australia). Connecting another shut-off valve (S2, Part No. SS- 42GS4, Swagelok, Australia) to the manifold, a union tee (Part No. SS-200-3, Swagelok, Australia), directs gas flow from the manifold to a vacuum pump. This enables the evacuation of the manifold line prior to the leak valve so that any excess reagents introduced via the septum can be removed from the gas flow.

A variable leak valve (VDL, VSE, Austria) meters the flow of helium through the manifold and into the ion-trap region of the mass spectrometer. This helium flow is coupled to an O3/O2 mixture via a union tee (Part No. SS-200-3, Swagelok, Australia). An ozone generator (Part No. HC-30, Ozone Solutions, USA) produces ozone which is split into an ozone destruct catalyst (ODC, Part No. 810-0008-03, IN USA Incorporated, USA) via a union tee (Part No. SS-200-3, Swagelok, Australia). Exhaust from the ozone destruct catalyst is fed into an exhaust inlet which vents the gases into a local building exhaust system. The rest of the O3/O2 mixture is directed to a restriction capillary (PRT, Part No. 0624226, 1/16 in. OD x 100 x 0.025 mm ID PEEKSIL™ tubing, SGE Analytical Science, Australia). This restriction samples the

O3/O2 mixture into the manifold. From the restriction capillary, the O3/O2 gas mixture is introduced to the helium flow via a shut-off valve (S3, Part No. SS-42GS4, Swagelok, Australia).

In the ozone generator trolley set-up, ozone gas is generated using high purity oxygen gas (Ocyl, Oxygen 4.0, Coregas, Australia) (Figures 2.4 and 2.5). The oxygen cylinder is connected to a mass flow meter (FM, Alicat Scientific, USA) via a 1/4 in. Teflon tubing and a 90° elbow fitting (Part No. SS-810-9, Swagelok, Australia). The mass flow meter is then connected to an ozone generator (Ozgen, Part No. HC-30, Ozone Solutions, USA). The ozone generator is an industrial scale ozone generator capable of producing up to 30 g h-1 of ozone. The ozone output is controlled using a potentiometer as well as varying the oxygen flow though the generator. The generated O3/O2 gas mixture flows through a gas line consisting of a shut-off valve

(S1, Part No. SS-42GS4, Swagelok, Australia) and a flow metering valve (SN, Part

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 63

No. SS-SS4, Swagelok, Australia). The flow metering valve enables the control of

O2 into the ozone generator so that the ozone output can be varied.

Figure 2.4: Schematic of the ozone trolley utilised in the ozonolysis experiments.

The ozone produced is measured by connecting the O3/O2 gas mixture flow into an ozone monitor (OzM, Part No. 106-H, 2B Technologies, USA). The ozone measurement is based on UV absorption and is capable of measuring high ozone concentrations (0.066 – 1.304 x 105 ppm). The UV photometer in the ozone monitor determines the amount of UV light absorbed by the ozone in the gas mixture passing through it. Using this information, the UV monitor measures the density (g m-3) which the ozone has at the arbitrary temperature and pressure inside the monitor. The ozone density can be compensated for temperature and pressure such that the mass of ozone present in one cubic meter of ozone gas under standard conditions (Temperature = 273.15 K, Pressure = 1 atm) can be determined.91 This compensated density has the units, g Nm-3 (grams per “Normal” cubic meter). The instrument also measures the concentration of ozone as weight percentage of ozone concentration in oxygen (% wt. O2). This measurement unit is typical of high concentration ozone monitors.

-1 -3 The ozone concentration is displayed either in g N m or % wt. O2. Typically, for ozonolysis experiments about 250 g N-1 m-3 of ozone is generated from oxygen gas flow of 0.1 standard litres per minute (SLPM) and adjusting the potentiometer to 65 units.

64 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

Figure 2.5: The ozone trolley in the laboratory. The trolley consists of an ozone generator, ozone monitor, flow adjustment valves and an ozone monitor.

Figure 2.6 shows the current layout of the instrumentation described in this section, as they are in the laboratory. The LTQ XL mass spectrometer rests on a table while the ozone mixing manifold is situated above it. The entire manifold is fastened securely on a breadboard (Figure 2.2). The ozone trolley can be disconnected and wheeled around for use with other mass spectrometers in the laboratory.

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 65

Figure 2.6: The current layout of the ozone mixing manifold, the LTQ mass spectrometer and the ozone trolley in the laboratory.

66 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

2.3 Ozone safety

The generation of ozone and the subsequent destruction was a vital part of the experiments outlined in this dissertation. All experiments were conducted in a busy laboratory setting comprising of different instruments and researchers. Adhering to the exposure standards for ozone in such a laboratory is of paramount importance for the safety of everyone working in the laboratory.

Ozone is a toxic, powerful oxidising gas and can have a deleterious impact on human health. The characteristic sharp pungent odour is recognised at concentrations from 0.01 to 0.04 ppm however, the nose rapidly loses its ability to detect ozone when exposed.92 Thus, odour should never be relied upon as a warning of high ozone concentration. Due to its highly oxidising nature, it reacts with tissues inside the respiratory tract and lungs, resulting in permanent, irreversible cell damage.93 Irritation of the eyes and dryness of the nose and throat occur when exposed to high concentration of ozone. When exposed to even higher concentrations of ozone, severe symptoms may arise such as tightness in the chest, shortness of breath or lethargy. These symptoms may persist for days and weeks after the initial exposure. Exposure to even higher levels could result in damaged lungs and .

In Australia, Safe Work Australia prescribes the workplace exposure standards for airborne contaminants. Exposure limitation to ozone is 0.1 ppm or 0.2 mg m-3 maximum limitation for an 8-hour time-weighted average; the average concentration of ozone must not exceed 0.1 ppm or 0.2 mg m-3 when calculated over an over an eight hour working day, for a five-day working week.94

Ozone generation was carried out using a based generator (HC-30, Ozone solutions, USA) actively monitored using an ozone monitor and the ozone concentration generated was up to 105 ppm. As such, the experiments were designed to generate sample and destroy (excess) ozone in a closed loop system. These high concentrations generated implies that several measures had to be put in place so that the ozone exposure remained well within the exposure standards: (1) Every gas-tight connection was checked for leaks with a liquid leak detector while passing oxygen gas only and, (2) once the ozone generator was active, a hand held

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 67

ambient monitor (Series 300, Aeroqual, New Zealand) ambient was used before finalising the experimental set-up. The hand-held monitor was also interfaced with the ozone generator such that if the detected concentration exceeded 60 ppb, the ozone generation was automatically switched off during experimental runs. The excess ozone generated was destroyed using either a destruct catalyst or a sodium thiosulphate ozone destruct solution, the destroyed ozone exhaust was then fed though the building exhaust duct system.

These measures ensured safe working laboratory conditions while generating, utilizing and destroying excess ozone within the laboratory.

2.4 Measuring reaction rate

The linear ion-trap used in this study is estimated to contain 2 × 104 ions at full capacity. 75 Operating pressure in the vacuum region is ca. 2 × 10-5 Torr and in the ion-trap itself the slow bleed of Helium gas (in normal mode of operation) delivers a pressure inside the trap of ca. 2.5 × 10-3 Torr or 8 × 1013 molecules cm-3. Neutral reagents can be added to the Helium flow (in ion-molecule mode of operation) up to a maximum of 0.1% before instrument performance (i.e., mass resolution and mass accuracy) is degraded. Thus for practical purposes reagents can be present at 106 – 1011 molecules cm-3.85 This large excess of neutrals over ions means reactions are observed under pseudo-first order conditions.

Pseudo-first order kinetic rate constant, k1, can be calculated by plotting the natural logarithm of the abundance of the reactant ion, [A]t, against the trapping time, t. The trapping time or the reaction time t is defined as the interval between the isolation of the mass-selected ion and the ejection of all the ions from the ion-trap for analysis. The resulting linear relationship with the slope equal to –k1, is given in equation (2.3). The slope is the pseudo-first order rate constant in the units of s-1.

[] = [] – (2.3)

68 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

The pseudo-first order rate constant when combined with the concentration of the neutral reagent, [N] according to equation 2.4, yields the second order rate constant. Alternatively, if the second order rate constant is known then it can be combined with the pseudo-first order rate constant to yield the concentration of neutrals, N, in the ion-trap.

() () = (2.4) []

2.4.1 Reaction efficiency

The ratio of the second-order rate constant k2 to the theoretical collision rate kcoll gives the reaction efficiency, Φ (Equation 2.6). In the gas phase, collision rates are dependent on the masses, the moments and polarizabilities of the reactants. 95 While dipole moments imply the separation of a charge, the polarizability of an atom or molecule describes the influence of an external field on the electron cloud.96 Since these properties are unique for each type of atom or molecule, it makes sense to use reaction efficiencies rather than the collision rates for comparative purposes. For instance, a reaction efficiency of 0.10 implies that 10% of the collision results in the formation of end products, while 90% of the collision results in dissociation to the reactants. The theoretical collision rates were calculated using the parameterised method of Su and Chesnavich.97 They utilized trajectory calculations and the empirical fit to the trajectory calculations gave the thermal capture . The trajectory collision rate is the value given by the multiplication of the Langevin collision rate, kL, and the thermal capture rate equation (Equation 2.5).

(.). ) = x (2.5) (..)

Φ= x 100% (2.6)

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 69

2.4.2 Temperature of the ion trap While there were firm theoretical arguments that the temperature of the ions in the ion trap were about 300 K, Gronert determined that the effective temperature in an ion trap was 310 ± 20 K.98 The temperature sensitive reaction between thiophenolate with 2,2,2-trifluoroethanol was used in a He bath gas at ~300 K. This implied that the temperature of the ions was slightly higher than the bath gas and the ion-molecule reaction in the ion trap occurs at near-thermal temperatures.

Blanksby and Harman in 2007 measured the temperature of casing containing the ion trap as 307 ± 1 K in a LTQ quadrupole ion trap.85 This temperature is taken to be the effective temperature of the quadrupole ion trap at which the ion-molecule reactions, presented in this thesis, occur.

2.5 Proof of principle ion-molecule reactions

- 2.5.1 Reaction of I + O3

In this section, observation and analysis of the reaction of ozone with iodide ions are reported as a proof of principle to demonstrate the effectiveness of the modifications previously described to the instrument in place. Also, this serves as an introduction to the reader to the typical ion-molecule reactions of ozone with iodide ions described in the following chapters.

In this experiment, the reaction of ozone with pre-selected iodide ions is used to observe any ion-molecule reaction products. A methanolic solution of potassium iodide was infused into the mass spectrometer and subjected to negative ion electrospray ionisation yielding abundant ions of m/z 127. These ions were then mass selected and trapped within the ion-trap in the presence of ozone for a period of time. To obtain the ion counts from the resulting mass spectrum, the ion peaks were integrated. The ion counts were subject to statistical analysis where the mean and the standard deviation for at least 50 scans was calculated. The data was then plotted with the standard deviations where necessary. The propagation of uncertainties was also calculated.

70 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

Figure 2.7 (a) and (b), shows the mass spectra obtained from trapping I- in the presence of ozone for 10 ms and 1000 ms respectively. After 100 ms an additional peak is observed in the spectrum at m/z 175 that increases in abundance from 5% to 20% of precursor ion abundance over 1000 ms. This observation is consistent with - the reaction of the iodide ion with ozone to form IO3 as previously described by Williams et al.77 The reaction was then carried out over a range of reaction times and the consumption and growth of the m/z 127 and m/z 175 ions monitored respectively. We could monitor the reaction for up to 10 seconds in contrast to the limitation imposed by using a selected ion flow tube.76 Normalization of the data was then carried out with respect to the total ion abundances. The resulting kinetic plot is shown in Figure 2.8 (a). The decrease in the normalised ion abundance of the precursor m/z 127 ion peak correspond with the increase in the normalised ion abundance of the m/z 175 product ion peak. Figure 2.8 (b) shows the log plot of the normalised abundance of the precursor ion m/z 127 as a function of reaction time. Applying a linear regression using the software Graphics Layout Engine (GLE) to the log plot gave the straight-line equation in the form of equation 2.3. The standard deviation in the slope was calculated using the LINEST (for linear functions) and LOGEST (for exponential functions) function in Microsoft Excel 2010 using the Analysis Toolpak.

Figure 2.7: The reaction of the iodide ions with ozone in the ion-trap for a pre- determined reaction time, (a) 100 ms and (b) 1000 ms.

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 71

Figure 2.8: (a) The normalised kinetic plot of the ozonolysis of the iodide (I-) ion. (b) The log plot of the precursor m/z 127 ion as a function of the reaction time. The linear regression fit was gives the equation of the straight line and the R2 value is also given.

The R2 value of 0.989 suggests the data are well fitted by the linear trend line. The gradient describes the pseudo-first order rate constant for the reaction of the iodide ion with ozone to be 0.264 ± 0.005 s-1 under the experimental conditions outlined. The second order rate constant for this reaction has been previously determined to be 1.0 ± 0.25 × 10-11 cm3 molecule-1 s-1. 14 Using this value together with the pseudo-first order rate constant obtained, the concentration of ozone in the ion-trap is determined to be 2.64 ± 0.08 × 1010 molecules cm-3.

The data points for the ln plot (Figure 2.8(b)) meanders along the straight-line fit. The explanation for this curvature will be given in Chapter 4 where the reaction between the I- ion and ozone is investigated in detail.

2.5.2 Control of O3 gas delivery

As described in the construction of the ozone mixing manifold (Figure 2.1 and 2.2), the restriction capillary allows the controlled flow of the O3/O2 mixture into the manifold where the gas mixture mixes with helium gas prior to entering the vacuum manifold of the mass spectrometer. Another way to control the concentration of ozone in the trap is by adjusting the amount of ozone generated at the ozone

72 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

generator. The manner in which these impact the concentration of ozone in the trap needs to be experimentally determined.

In the experiment described previously, a PEEKsil restriction capillary (SGE Analytical Science, Australia) of length 100 mm (25 µm inner diameter) was used. To investigate the effects, the tubing had on the final concentration of ozone delivered to the ion-trap in the mass spectrometer, two different lengths of PEEKsil tubing were used (50 mm and 100 mm, both 25 µm inner diameter).

The ion abundance of the m/z 127 and 175 ions was plotted as a function of trapping time of the m/z 127 ion to observe the kinetics of the reaction (Figure 2.9). Using a shorter restriction tube, the half- i.e. time taken for the reactant ion abundance to be reduced to 50% of its initial ion abundance, was 0.9 s while for the larger restriction tube, the half-life was 3.3 s.

Subsequently, plotting the natural logarithm of the reduction of the [I-] ion abundance as a function of reaction time and subsequently fitting the data with a straight line gives the pseudo-first order rate constant for the reaction (Figure 2.10). Using the published second order rate constant for the reaction between [I-] ion and -11 3 -1 -1 ozone (1.0 ± 0.25 × 10 cm molecule s ) , the concentration of [O3] in the ion- trap is determined for both cases. 77

The shorter restriction tubing enabled the concentration within the ion-trap to be 5.30 ± 1.33 × 1010 molecules cm-3. Using the longer restriction tubing resulted in the ion-trap concentration of ozone to be 2.0 ± 0.5 × 1010 molecules cm-3. This value is different from the value obtained in the previous section of the reaction between iodide ions and ozone which was 2.64 ± 0.08 × 1010 molecules cm-3. This is because, the experiments were run on different days and the ozone concentration generated was slightly different. Thus, by using shorter restriction tubing, the amount of ozone within the ion-trap can be increased 2.65 times. Varying the length of the restriction tubing allowed an extra dimension of control of the ion concentration in the ion-trap.

Using the 100 mm restriction tube, the amount of ozone generated was varied to investigate if the pseudo-first order condition was maintained when utilizing

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 73

different ozone concentrations in the experiments for the reaction between the iodide ions and ozone. As mentioned previously, ozone was generated externally using an ozone generator and the amount of ozone in the ion-trap can be varied by varying the length of the restriction capillary and also the amount of ozone generated externally.

Figure 2.11 shows the linear relationship between the –log of the precursor ion (m/z 127) and the reaction time(s) employed across the three different ozone concentration used.

Figure 2.9: Plots of the normalised ion counts against the reaction time of the decay - - of the I (m/z 127) ion and the growth of the IO3 (m/z 175) product ion using the (a) 50 mm and (b) 100 mm restriction. The mean and standard deviation for at least 50 individual scans are plotted for each reaction time. The break in the data represents a data point which was erroneously uncollected.

Figure 2.10: Comparison of the pseudo-first order rate constants of the reaction - between I and O3 when using the 50 mm restriction and the 100 mm restriction.

74 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

Figure 2.11: Plots of the natural logarithm of the abundance of the m/z 127 ion (normalised to the total ion count) at reaction times between 0.01 s and 10 s. Data from 3 different concentrations indicated in the plot are measured external to the ion- trap mass spectrometer.

As expected, the highest pseudo-first order rate constant of 0.271 ± 0.0005 s-1 was obtained when using the highest ozone concentration generated which was 260.4 g Nm-3. When using the ozone concentration of 187.0 g Nm-3, the pseudo-first order rate constants was 0.199 ± 0.002 s-1, and 0.039 ± 0.004 s-1 when using the lowest ozone concentrated generated, 47.1 g Nm-3. Using these values for the pseudo-first order rate constants together with the published second order rate constant (for the reaction between the iodide ion and ozone (1.0 ± 0.25 x 10-11 cm3 molecule-1 s-1), the concentration of the ozone in the trap under these different ozone concentrations generated was determined. 77

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 75

3E+10 ) 3

2.5E+10 y = 1E+08x R² = 0.9958 2E+10

1.5E+10

1E+10 concentration (molec/cm 3 5E+09

Internal O Internal 0 0 50 100 150 200 250 300 3 External O3 concentration (g/Nm )

Figure 2.12: Plot for determination of the internal ozone concentration in the ion- trap for a given external ozone concentrated generated. The equation of the liner fit as well as the R2 value is stated. This relationship is only valid when using a long - (100 mm) restriction tube and is benchmarked for the I + O3 reaction.

Generation of 47.1 g Nm-3 of ozone externally and passing it through the ozone mixing manifold and to the ion-trap region of the mass spectrometer resulted in the ozone concentration in the trap to be 3.9 ± 0.68 × 109 molecules cm-3. Likewise, generating 187.0 g Nm-3 and 260.4 g Nm-3 of ozone resulted in the ion-trap ozone concentrations of 1.99 ± 0.50 × 1010 and 2.71 ± 0.11 × 1010 molecules cm-3 respectively. Thus, a graph depicting a relationship between the externally produced ozone concentration and the internal ion-trap ozone concentration was plotted and is given in Figure 2.12. This allows one to estimate the amount of ozone in the ion-trap given the amount of ozone generated externally.

Effectively, the combined use of the 100 mm restriction tube and the different ozone concentration generation allows for an order of magnitude of variation in the amount of ozone eventually in the ion-trap region. This narrows the useful concentration of ozone for experimental purposes in the ion-trap.

76 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

2.5.3 Reproducibility of ozone delivery

Almost any analytical instrument is subject to some drift. For instance, for the ozone detector employed, which uses a photometric UV determination of ozone, changes in the UV lamp intensities will affect the ozone measurement readings. This is possible if the lamp needs replacement or if the absorption cell itself is dirty. Such instances can be a source of uncertainly in the ozone measurement. This deviation (a drift) from the actual concentration to what is measured may result in different ozone concentration in the ion-trap region of the mass spectrometer. This results in errors in determining accurate pseudo-first order rate constants. Certain ozonolysis reactions can be inherently slow, thus, the trapping time can be long (>10 seconds per scan required) to obtain any meaningful kinetic data. Thus, the experiment can be prolonged when collecting data for slower reactions.

Figure 2.13: Normalised ion count plots of the reaction between the iodide ion and ozone at the (a) start and (b) end of the day. Exponential functions were fitted for the m/z 127 data points and the equation of the fit and the R2 values are given.

To test the effects of experimental drift, if any, the reaction of ozone with the iodide ion was carried out at the start of the day under low ozone conditions (12.0 g -3 Nm O3 generated) using a 100 mm restricting tube. This experiment was repeated at the end of the day (5-6 hours later). The resulting data was normalised to the total ion count and the resulting comparison plot is shown in Figure 2.13. It can be appreciated that there is minimal drift in the gradient of the exponential decay curve. Therefore, we are confident that the data collected for slower ozonolysis reactions will be free of errors at least from those resulting from experimental drift.

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 77

2.6 In-source ozonolysis

In the previous section, a method of studying the reaction kinetics of an ion- molecule reaction between a pre-selected iodide ion and ozone was described. Introduction of ozone into the ion-trap of the mass spectrometer through an ozone mixing manifold enabled this ion-molecule reaction to occur. Also, adjusting the amount of ozone generated and the use of the restriction capillary allowed some control over the useful concentration of ozone used in the experiments. However, for fast ion-molecule reactions, using high concentration ozone (109 – 1010 molecules cm-3) can lead to a prompt conversion of precursor ions to product ions. In such cases, the half-life of the reaction may be much shorter than the shortest trapping duration allowed by the instrument (i.e., t1/2 << Ion-trapping time). Therefore, meaningful kinetic data cannot be obtained. A way to monitor such ion-molecule reactions using much lower concentration of ozone is ideal for such cases.

During ionisation at the ESI source, the solvent containing the analyte is dispersed into an electrospray. Together, the sheath, auxiliary and sweep gas valves control the flow of nitrogen into the ESI interface which functions both as a nebulising gas and a desolvation gas. The fine mist produced by the high voltages employed, exits the sample tube and the auxiliary gas which works in tandem with the sheath gas in nebulising and evaporating sample solutions. The sweep gas flows out from behind the sweep cone in the ESI interface and it aids in declustering and reduction of the formation of adducts.76

Ions produced during the ESI process can participate in chemical reactions at the ESI interface. Mann and co-workers reported an oxidation product, [M+H+16]+ ion, during ionisation of peptide fragments using positive ion ESI under high source voltage conditions. They attributed the additional 16 Da mass to the addition of atomic oxygen to the proteins.99 Maleknia et al. described an approach to achieve radical-induced oxidative modifications of proteins at the ESI interface (in- source).100 This technique relied upon using oxygen gas as the nebulising gas under positive mode ESI and using a very high ESI source voltage of 8 kV. Thomas et al.

78 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

applied this technique but under negative mode ESI for the in-source oxidation of phospholipids. When methanolic solutions of a phospholipid were sprayed under similar conditions (utilising oxygen as a nebulising gas and -6 kV source voltage), ozonolysis products of the phospholipid in the mass spectra was observed.101 Under such conditions, a corona discharge similar to the one shown in figure 2.14 was observed.

Figure 2.14: The onset of discharge when employing high spray voltages (8kV) and using oxygen gas as the nebulising gas in the ESI interface.

Ozone production during corona discharge is well-known and this process is analogous to the production of ozone in the atmosphere during strikes. Furthermore, it has been found that such discharges generated under negative polarity produce significantly more ozone than generated under positive polarity.102,103

To demonstrate that iodide ions can be oxidised at the ESI source when employing oxygen as the nebulising gas and using high voltages, a solution of iodide in water was sprayed under negative mode ESI. The resulting qualitative plot is shown in figure 2.15. As the source voltage is increased from 3 kV progressively to 8 - kV, the abundance of the m/z 127 peak diminishes but the m/z 175 (IO3 ) peak rises. The iodide ion was being oxidised in-situ to the iodate ion.

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 79

Figure 2.15: The relative abundance of the m/z 125 iodide ion and the ozonolysis product m/z 175 ion as a function of spray voltage.

This, in-situ, generation of ozone gas allows the reaction between ozone and compounds of interest which are sprayed from the ESI spray needle. Such reaction products are quickly ionized in the source and they can be observed in the mass spectra acquired. The ozone generated is in sufficiently low concentrations and the method can be very useful in probing the products derived from fast ozonolysis reactions. Since the ozone is produced locally at the ESI interface, any excess ozone produced is pumped away through the ESI source exhaust.

2.7 Aerosol chemistry experiments

Organic aerosols constitute a major fraction (> 50%) of total aerosol mass. Although, many compounds in organic aerosols have been characterised, sufficient knowledge of the composition of aerosols is still severely lacking due to their extreme spatial and temporal variations. Furthermore, atmospheric concentrations of sample amounts are only typically a few micrograms per cubic meter.104 Aerosols have an overall net cooling effect on the atmosphere therefore affecting the energy balance of the Earth’s atmosphere, which in turn influences .15

80 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

Aerosol particles also affect health, continual exposure to these particles has been linked to increased mortality from respiratory and cardiovascular diseases.105,106 New methods which help to characterise these complex mixtures are actively sought. A method utilising real-time extraction is attractive for the analysis of such complex mixtures compared to the traditional ‘off-line’ methods.

Off-line methods usually comprise of sampling, chromatographic separation and/or extraction and analysis aspects. Usually each of these steps takes place on hours to days’ time scales and during these prolonged processes, the samples suffer from losses as well as unwanted secondary reactions on collected samples.107 Most atmospheric processes occur in the seconds or minute timescales and by utilizing such methods; the unique chemical fingerprint is lost during sampling. Online methods which provide near real-time, highly time resolved aerosol composition data are attractive prospects in understanding the dynamic chemical composition of organic aerosols in the atmosphere.

In this section, the construction and testing of a system to generate secondary organic aerosol (SOA) from the interaction of alkenes and ozone in the gas phase is described. The aim was to develop an experimental set-up capable of direct, on-line analysis of vapour and aerosol phase products using an electrospray ionisation mass spectrometer. The configuration is based on prior efforts of the Kalberer and Laskin groups.108,109

Preliminary experiments were carried out to observe if a vapour of a compound (1-cyclohexene carboxylic acid (1-CCA)) could be transported by a carrier gas into the ionizing region of the mass spectrometer. The use of nitrogen gas facilitated this transport of the neutral compound into the ESI interface. As shown in Figure 2.16, the Nitrogen Gas (Coregas Nitrogen 4.0, Australia) was connected to a flow-meter (Key Instruments, USA) via a Teflon 1/4” tube. The flow-meter and the Schott bottle were held upright. The flow-meter enabled the control of the flow of the

N2 gas (1 SLPM) into the Schott bottle containing the 1-CCA compound (97% purity, Sigma-Aldrich, Australia) dissolved in methanol (0.5 mL of 634 µm 1CCA in MeOH). Two holes were drilled in the cap of the Schott bottle, one for the incoming

N2 gas line and the other for the N2 and 1-CCA vapour mixture going into the ESI

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 81

spray source. The hole was sealed with black duct-tape after connecting the tubes into the Schott bottle. The line containing the N2 and 1-CCA vapour was directed into the side of the ESI interface with the help of a retort stand. Negative mode ESI was employed using methanol as the spray solvent supplied at 10 uL min-1. The spray voltage used was 3.5 kV.

Figure 2.17(a) shows the negative ion spectra obtained when spraying MeOH as the solvent in negative mode while having N2 flow on through the empty Schott bottle. This spectrum is typical of negative mode ESI-MS in the absence of an analyte. The dominant m/z 125 signal likely arises from a fatty acid contamination. Figure 2.17(b) shows the spectrum obtained when 1-CCA is present in the Schott bottle. The spectrum shows an abundant ion at m/z 125 corresponding to the [M-H]- ion from 1-CCA.

Figure 2.16: The experimental set-up for the 1-CCA pick-up experiment consisting of a nitrogen gas source, a flow-meter, a beaker and a retort-stand holding the + N2 vapour line into the ESI interface.

82 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

This shows that the N2 gas had successfully picked up the 1-CCA into the

ESI region and ionisation had taken place. When the N2 gas is switched off at the flow meter (Figure 2.16), the m/z 255 peak is once again the base peak and the m/z 125 peak is at 30 % relative abundance to the base m/z 255 peak as shown in Figure 2.17(c).

Figure 2.17: Individual spectra obtained during (a) Blank, (b) N2 flow on and (c) N2 flow off conditions of the experiment.

Figure 2.18 shows the responsiveness of the system to a change in the N2 flow. Switching on the N2 flow causes a drastic rise in the signal for the m/z 125 ion. The ion signal subsequently diminishes because of the reduction in the amount of vapour left in the Schott bottle as a result of the pick up by the N2 carrier gas. As the

N2 flow is switched off, the ion signal is reduced. There are still some ions left even though the N2 flow is off; this is probably because of ions lingering in the ESI interface.

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 83

This experiment successfully demonstrated the uptake of a compound from a Schott bottle into the ESI source of the mass spectrometer using a carrier gas. In the next set of experiments, this idea that a carrier gas can be utilized to carry compounds through to the ionising region of the mass spectrometer is explored and applied to the in-situ generation and subsequent online-analysis of aerosol.

Figure 2.18: (-) ion TIC for the m/z range 124.5-125.5. The dotted lines show the onset of the switch in N2 flows during the experiment. Switching on the N2 flow results in increased ion signal. This is due to the appearance of m/z 125 ions in the spectra shown in Figure 2.17(b). Switching the N2 flow off causes the ion signals counts to diminish.

2.7.1 Aerosol generation and analysis

Figure 2.19 shows the schematic of the online aerosol generation and analysis set-up. The flow of high purity Oxygen gas (Coregas 4.0, Australia) was directed into flow-meter (FM1, Key Instruments, USA ) and the flow was then split using a union tee (T1, Part No. SS-200-3, Swagelok, Australia). These split flows were then connected to another two flow-meters (FM2 and FM3, Key Instruments, USA); one

84 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

of these flow-meters was connected directly to an ozone generator (1000BT-12, Enaly, USA) and the other flow-meter was connected to the output from the ozone generator via a union tee (T2, Part No. SS-200-3, Swagelok, Australia). The union tee, T2, was connected directly to a “reaction chamber” (250mL Schott bottle) which had a modified cap. The modified cap enabled a leak-free fitting for the in-coming

O3/O2 and the out-going O3/O2/aerosol gas lines. Subsequently, the reaction chamber was connected to an ozone monitor (Model 106 ozone monitor, 2BTech, USA) .

Figure 2.19: The schematic of the online aerosol generation and analysis experimental set-up.

Through another union tee (T2, Part No. SS-200-3, Swagelok, Australia), the line from the reaction chamber was also connected to a condensation particle counter

(Model 3022, TSI, USA). A 3-way valve (V3-way, Part No. SS-42GXS4, Swagelok, Australia) connected the line from the reaction chamber to the filter holder (LS-47,

Adventec MFS, Inc., Japan) and also to a union tee (T3, Part No. SS-200-3, Swagelok, Australia). The 3-way valve enabled the switching of the flow from the reaction chamber either towards the filter holder or towards the ESI inlet.

Figure 2.20 shows the installed aerosol guide at the side of the ESI source.

While the aerosol line was crudely directed into the ESI interface during the N2 experiments by using a retort stand in the preceding section, here, a modification to the ESI source was carried out. For instance, the ESI source has a cylindrical 35mm glass panel on its side which can be removed. The glass panel was removed and replaced with a custom designed Teflon aerosol guide manufactured at QUT.

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 85

Figure 2.20: The installation of the aerosol line guide on the side of the ESI inlet. The front panel is open to show the aerosol flow line protruding out of the aerosol line guide. The aerosol flow line is inserted into the aerosol line guide and is sealed with Teflon tape to prevent outflow of gas from the ESI source.

Also, shown in Figure 2.20 is the ESI source exhaust at the bottom of the picture which leads to the ozone scrubber. The ozone scrubbing solution is made up of a reducing agent, sodium thiosulfate (Na2S2O3) and potassium iodide (KI) in water. In solution, the ozone oxidises the iodide ions to I2 and the thiosulfate reduces 110 the I2 back to iodide ions (Equations 2.7 and 2.8). The reactions induce a colour change from a clear solution to a light brown solution and provide a visual clue for the reducing reaction. Darker colours indicate that the scrubber solution be replaced with a fresh solution. The exhaust was then vented to the laboratory exhaust system.

86 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

+2 + ⇋ + +2 (2.7)

2 + ⇋ +2 (2.8)

2.7.2 Proof of concept aerosol generation experiment

50 uL of d-Limonene (97% purity, Sigma-Aldrich, Australia) was injected via a 1.5 mm hole on the Schott bottle cap with ozone continuously supplied to the reaction bottle. Figure 2.21 shows the differences in the spectrum before and after the d-Limonene injection.

Before injection, the spectrum is typical of a negative mode ESI-MS in the absence of an analyte described previously. After injection, the spectrum profile changes and there are three different humps between the ranges m/z 150 – 300, m/z 300 – 450 and m/z 480 – 600. These features are similar to published results of the mass spectrum of secondary aerosols formed from limonene ozonolysis.108,111 These papers attribute these clusters of peaks to monomers, dimers and tetramers of the secondary aerosol products from limonene ozonolysis.

Figure 2.21: The profile changes before the addition of d-Limonene to the reaction bottle and after the addition. Successful generation and ionisation of aerosol compounds is indicated by the presence of three major clusters of peaks.

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 87

This is indicative of the successful generation of the d-Limonene ozonolysis products and their subsequent ionisation within the ESI source. The results of these experiments and its applications in the formation of aerosols from 1-CCA ozonolysis are explored and discussed in more detail in the results section of this dissertation.

88 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

Chapter 3: Ozonolysis of cyclohexene carboxylates

3.1 Introduction

Ozonolysis of volatile organic compounds (VOCs) is an important oxidation initiation reaction and is known to contribute significantly to oxidative processing in the atmosphere. The subsequent oxidation products can condense on pre-existing particles forming secondary organic aerosols (SOA) that are known to affect the Earth’s radiation budget either by scattering incoming solar radiation or acting as cloud condensation nuclei.112 The ozonolysis of biogenic terpenes such as α-pinene and limonene (Figure 3.1) have a profound effect on SOA formation. The total biogenic organic emissions are thought to exceed estimated anthropogenic emissions by an order of magnitude.113 SOA formation from these compounds is estimated to range from 25 to 210 TgC yr-1 (1 TgC = 1012 grams carbon).15 For instance, in many parts of Europe it is reported that up to 90% of total SOA originates from biogenic sources.113

Figure 3.1: Structures of endocyclic alkenes: a) α-Pinene, b) Limonene c) Cyclohexene and d) Cyclohex-1-ene-1-carboxylate anion

Oxidation of cycloalkenes by ozone has been recognised as an important contributor to the organic fraction of SOA. 114 Various groups have studied the cyclohexene ozonolysis mechanism and product distributions. The cyclohexene system is an ideal symmetrical model system for investigations concerned with the ozonolysis of endocyclic alkenes. In these studies, both gas and particle phase

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 89

products have been identified in the ozonolysis of cyclohexene.115,116 These compounds include oxo-carboxylic acids, di-carboxylic acids, hydroxyl-carboxylic acids and aldehydes (Figure 3.2).

Figure 3.2: Some gas phase products identified from the ozonolysis of cyclohexene.115,116

Termed the ‘Criegee mechanism’, which was formulated by Rudolf Criegee, the fundamental step involves a 1,3-cycloaddition reaction between the ozone 1,3- dipole and the alkene forming a primary ozonide (Scheme 3.1).117 The primary ozonide is thought to have a 1,2,3-trioxolane structure, initially inferred through NMR and IR studies of the ozonolysis of different alkenes.118,119 Furthermore, the van der Waals (vdW) complex between ozone and has been observed using microwave spectroscopy.120,121 This structure of the complex has been corroborated initially using low-level theoretical methods.7,122 The primary ozonide then decomposes via the O-O and C-C bond homolysis giving two decomposition products depending on which O-O bond is broken. These products are formed with high nascent energies and can undergo stabilisation by collisions with other molecules. These stabilized molecules (CI1 and CI2 in Scheme 3.1) have a carbonyl oxide (also called a Criegee intermediate) and a carbonyl moiety in their structure. In contrast, for linear alkenes, the formation of POZ during ozonolysis and the

90 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

subsequent decomposition results in the formation of the carbonyl oxide that is separated from the carbonyl compound. Compounds CI1 and CI2 can subsequently participate in other reactions such as intra-molecular rearrangements and secondary reactions.

Bailey and Lane highlight that the alternative mechanism to the ozonolysis mechanism of Criegee exists which was inferred from the formation of “partial cleavage” products such as an epoxide.123 Comparing the ozonolysis mechanism for ethene and based on calculated Arrhenius factors, De More suggested that the transition states of these reactions are fundamentally different.124 The initial step of the “DeMore mechanism” involves the reaction of ozone with either of the in the double bond resulting in the formation of a diradical transition state which can either yield an epoxide and molecular oxygen or the primary ozonide depending on the geometry of the transition state (Scheme 3.1).

While the Criegee mechanism has been used to explain a large number of ozonolysis reactions in both the solution and gas phases, the DeMore mechanism has been used to explain the formation of epoxides and other secondary products during ozonolysis. There is evidence to indicate that both the mechanisms can compete efficiently.125 Computational study on the first steps of the ozonolysis reaction of acetylene indicates that the reaction is competitive between Criegee and DeMore mechanisms while the ozonolysis of tetrafluoroethylene and hexafluropropylene is thought to be dominated by the DeMore mechanism.126 Such data suggests that the mechanism which is favoured depends on the properties of the groups adjacent to the double bond. Ozonolysis of alkenes with large steric hindrance in the solution phase results in epoxides as the major product.9 In the gas phase, epoxide formation can also result from the decomposition of the primary ozonide in the case for ethylene to 1 127 yield an oxirane and O2. The formation of 1,2-epoxy-3-butane from the ozonolysis of 1,3- has also been attributed to the dissociation of the primary ozonide.128,129 There is no reported evidence for the formation of singlet oxygen from ozonolysis reactions of alkenes, however, epoxides are formed in those experiments.130

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 91

Ozonide formation is typically exothermic by more than 50 kcal mol-1 for the reaction between ozone and alkenes. Using the high level QCSID(T)/6- 311++G(d,p)//MP2/6-311++G(d,p) method, the exothermicity for the ethene and ozone reaction was determined to be 48.9 kcal mol-1. 131 The B3LYP and the CCSD(T) methods using the basis set (6-31G(d,p)) showed that the primary ozonide is nested below the reactions by about 57.3 kcal mol-1 and 52.5 kcal mol-1 respectively.15 The weakly bound vdW complex is about 0.74 kcal mol-1 below the reactants and the subsequent transition state is calculated to be about 2.5 kcal mol-1 above the entrance channel. Recent theoretical methods are in excellent agreement with the experimental activation energy of 5 kcal mol-1.120,121

The ozonolysis of charged compounds has not gained much attention compared to neutral compounds. In ion-molecule studies of ozonolysis, charged adducts have a profound influence on the rate of ozonolysis.132 Charged isomeric compounds which only differ structurally on the basis of their double bond position also exhibit different ozonolysis rates.90 Furthermore, even for neutral ozonolysis systems, the identity of the intermediates in these reactions still remains elusive. Therefore, a study of the ozonolysis of charged compounds to further understand how different it is from neutral ozone chemistry as well as to further probe the intermediates in such reactions is necessary.

92 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

Scheme 3.1: The first steps of ozonolysis of cyclohexene via the Criegee and

DeMore mechanism. The reactants, transition state of the cycloaddition (TSCG) and the product, primary ozonide (POZ) is shown for the Criegee mechanism. DeMore mechanism highlights two transition states, exo-TSDM and endo-TSDM with the resulting products, epoxide and molecular oxygen and primary ozonide (POZ) respectively. The decomposition pathways (a) and (b) of the POZ results in the

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 93

formation of compounds CI1 and CI2 which can participate in other reactions. CI1 and CI2 can undergo 1,3-dipolar cycloaddition to form secondary ozonides (SOZ).

The modified mass spectrometer allows the introduction of neutral gases into the ion-trap. Once the precursor ions are mass selected, this facilitates, for instance, the kinetic studies of the reaction between distonic ions and di-oxygen.133 Using this charge tagged approach, the reaction of ozone with a mass selected, precursor ion in the gas phase can be observed. By introducing ozone into the ion-trap region of the mass spectrometer, the well-defined Criegee products have been readily observed in the ozonolysis of ionized lipids.134 The technique has been particularly useful in both the structure elucidation and selective detection of conjugated C=C double bond motifs within lipids.

An endocyclic alkene tethered to a carboxylic group, 1- & 3-cyclohexene carboxylate (1- & 3-CCA), was chosen as model compounds to study the ozonolysis reaction. Structurally, it is similar to the monoterpenes limonene and α-pinene which are efficient SOA sources.135 The isomers allows for direct comparison of reaction products, kinetics as well as the energetics of the ions and ozone reaction using a combination of experimental and density functional theory (DFT) calculations. In this part of the dissertation, the utility and versatility of mass spectrometry in probing the ozonolysis reaction of a charge tagged monoterpene analogue is tested. Furthermore, the utility of using a charged tagged model compound as a surrogate for an endocyclic monoterpene is also tested.

3.2 Methods

3.2.1 Materials

1- and 3-Cyclohexene carboxylic acid (Sigma-Aldrich, St. Louis, MO, USA) were purchased from commercial suppliers and were used as received. Methanol was HPLC grade (APS Chemicals, Sydney, Australia). High purity compressed oxygen (Oxygen 4.0, purity 99.99%) and ultra-high purity helium (Helium 5.0, purity 99.999%) were obtained from Coregas (Yennora, Australia).

94 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

3.2.2 Instrumentation

Experiments were conducted on a linear ion-trap mass spectrometer (LTQ- XL, ThermoFisher Scientific, San Jose, CA, USA) that has been modified to allow ozone gas to enter the ion-trapping region. To generate [M-H]- anions of selected carboxylic acids, the precursor acid dissolved in methanol (ca. 50 μM) and infused into the electrospray ionization source of the instrument with a flow rate of 10 μL min-1. The instrument was operated in negative ion mode using a spray voltage of 5 kV; a capillary voltage of 27 V; a tube lens voltage of 170 V; and the temperature of the heated transfer-capillary was set to 275 °C. For tandem mass spectrometry experiments ions were mass-selected using an isolation width of between 1 and 5 Th. For collision-induced dissociation, selected ions were subjected to a normalised collision energy of between 15 and 30 (arbitrary units) for an activation time of 30 ms. For gas phase ion-molecule reactions, normalised collision energy was set to 0. Activation times of between 30 and 9,000 ms were set representing the reaction time. For gas phase ozonolysis reactions, ozone was introduced into the flow of UHP helium (Coregas, Yennora, Australia) via a gas-mixing manifold as described in Chapter 2 of this dissertation. 250 g Nm-3 of Ozone was generated from oxygen gas (99.99%, Coregas, Yennora, Australia) using an ozone generator (HC-30, Ozone Solutions, Sioux Centre, Iowa, USA) and introduced to the helium flow using chemically inert PEEKsil tubing (100 mm, 25 µm I.D., SGE Analytical Science, Australia). The helium gas was supplied via a variable leak valve (Granville-Phillips, Boulder, CO, USA) to maintain an ion gauge pressure of ca. 0.70 x 10-5 Torr. All spectra presented were acquired using the instrument control software (Xcalibur 2.0, Thermo Fisher Scientific) and represent an average of at least 50 individual scans.

3.2.3 Statistical analysis

The mean and the standard deviation were calculated from at least 50 scans for a single data point. The standard deviation is included in the data plots. Exponential fits were carried out on the GLE (Graphics Layout Engine) software and the standard deviation of the slope of the exponential fits was carried out using LOGEST function and linear fits using the LINEST function in Microsoft Excel 2010 using the Analysis Toolpak. Propagation of statistical errors was calculated and is given when necessary.

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 95

3.2.4 Computational method

All the calculations are performed using the Gaussian 09 program packages.136 The geometries of all the reactant, products, intermediates and transition states are optimized using the hybrid density functional theory (B3LYP) method in conjunction with the 6–31+G(d,p) basis set.137,138 The choice of the theory and basis sets is outlined in the benchmarking of computational method section in Appendix A. In summary, the method selected was used to benchmark against the calculations obtained by Vayner et al. who used the high level CCSD(T)/cc-pVTZ theory to study the post-transition state intramolecular and unimolecular dynamics for ozonolysis.139 In that particular study, similar heats of formation (ΔH) were obtained for the ozonolysis of propene using the hybrid DFT method B3LYP/6–31G(d) and the coupled-cluster method CCSD(T)/cc-pVTZ for the formation of the primary ozonide (60.2 kcal mol-1 vs 62.0 kcal mol-1). Additional theoretical investigation was done on the charged system comprising of the propenoate anion and ozone. The energies for the formation of the primary ozonide from the propenoate anion and ozone was calculated using hybrid DFT methods and single point energies were calculated from these geometries. The results are given in section A.2 in the appendix.

Due to the multi-configurational nature of the Criegee intermediate, the potential energy surface may be suited to a multi-reference method.140,141 However, these computationally intensive methods were not employed in the present study but could be the subject of future investigations.

Frequency calculations were performed at the same level to check the obtained species is an intermediate (with all real frequencies) or a transition state (with one and only one imaginary frequency) and to characterize zero-point vibrational energy (ZPVE). To confirm the transition state connects designated intermediates, intrinsic reaction coordinate (IRC) calculations were performed at the B3LYP/6–31+G(d,p) level of theory. All the species in this study are in the singlet state unless otherwise labelled. The energies are given in kcal mol-1 and the vibrational frequencies that contribute to the thermal corrections are scaled by 0.9648.142 The cartesian coordinates of selected optimised structures are given in the Appendix section A.3.

96 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

3.3 Results and Discussion

3.3.1 Overview of the experiment

Figure 3.2 shows the overview of the ion-molecule experiment carried out in this section. Negative ions were produced in the ESI interface and directed into the ion-trap of the mass spectrometer. The ion-trap contained a mixture of He as the buffer gas as well as O2/O3 mixture which was introduced into the ion-trap through a mixing manifold as described in Chapter 2 of this dissertation. The mass spectrometer continually scans out the ions resulting in a full-MS spectrum (a). Once the ion of interest was identified, it was mass selected. In this stage, the mass spectrum showed a single peak (b). The ion was trapped for a given amount of time so that ion-molecule reactions can occur with ozone. After that time had elapsed, if the ion molecule reactions had occurred, the spectrum should show new peaks indicating ionic products formed from the ion-molecule reaction.

Figure 3.3: Overview of ion-molecule reaction stages between ozone and pre- selected ions in the ion-trap mass spectrometer. Different scan-out stages in the ion- trap are labelled as MSn. The corresponding representative spectrums are also given. (a) Represents the full-MS scan, (b) represents the isolation scan for the mass- selected isolated ion and (c) represents product-ion scan following entrapment of ions in the presence of ozone for a given amount of time (1.5 s in this example) showing the appearance of new peaks.

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 97

3.3.2 Benchmarking of ozone concentration in the ion-trap

The reaction of iodide ions with ozone was used to benchmark the concentration of ozone in the ion-trap as outlined in Chapter 2 of this dissertation. The pseudo first order rate constant of the reaction was determined to be 0.264 ± 0.005 s-1. The second order rate constant obtained from the literature for this reaction is 1.0 ± 0.25 × 10-11 cm3 molecule-1 s-1. The ozone concentration in the ion-trap is the ratio of pseudo-first order rate constant and the second order rate constant for the reaction, therefore the concentration of ozone in the ion-trap was determined to be 2.64 ± 0.08 × 1010 molecules cm-3.

3.3.3 Ozonolysis of 1-CCA-H- and 3-CCA-H- ions

Electrospray ionisation of methanolic solutions of 1- and 3-cyclohexene carboxylic acid yielded abundant ions at m/z 125. The negatively charged ions are herein defined as 1-CCA-H- and 3-CCA-H- and the neutral forms of these carboxylates are referred to as 1-CCA and 3-CCA. Isolation of the m/z 125 ion within the ion-trap, in the presence of ozone yielded unique products (MS2). These ions were trapped under the same O3 concentration. By varying the isolation time, the amount of time these ions were exposed to the ozone molecules was adjusted. Thus, subsequent growth of reaction products when the ions are trapped for longer reaction times was observed. Figure 3.4 shows the changes in the spectra for 1- and 3-CCA-H- ozonolysis (left and right panels respectively) when the precursor [M-H]- ion is trapped for 1, 4 and 9 seconds. At a reaction time of 1s, 1-CCA-H- ozonolysis yields products with m/z 60, 139 and 141. However, for the 3-CCA-H- ozonolysis, there is a lack of any major products.

98 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

Figure 3.4: Mass spectra of the ozonolysis of 1- and 3-CCA-H- ions, m/z 125, as a function of reaction time between the mass ranges of m/z 50 to 200. Only the spectra resulting from a reaction time of 1, 4 and 9 seconds for each species are shown for comparison.

When the trapping time is increased to 4 s, the major peak for 1-CCA-H- ozonolysis is the m/z 60 peak followed by peaks at m/z 141 and 139. The precursor peak at m/z 125 is reduced to less than 50% of the m/z 60 peak as the precursor ion is being converted to the product ions. Furthermore, the ion counts are diminished as the reaction time is increased. This loss in charge is also evident for the 3-CCA-H- ozonolysis but in this case, the reaction fails to yield any major products even at a reaction time of 4 s. At the reaction time of 9 s, for 1-CCA-H- ozonolysis, the m/z 125 peak diminishes further relative to the major product peaks. At that same reaction time, the 3-CCA-H- ozonolysis does not product any significant product ions.

By normalising the average ion counts for each isomer to the maximum ion and plotting the counts against the reaction time, the reaction profiles of these two

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 99

isomers can be directly compared. Using a single-term exponential model, the data points for the normalised ion counts are fitted as shown in Figure 3.5.

Figure 3.5: Data points resulting from reaction time of 0.3 to 5 seconds are fitted using a single-term exponential function for both 1- and 3-CCA-H- ion ozonolysis. The error bars represent standard deviation of the data points for at least 50 acquired scans.

The half-life for the 1-CCA-H- precursor ion ozonolysis is determined to be 0.43 s whereas for the 3-CCA-H- precursor ion is 4.31 s. This increased reactivity is mirrored by a larger loss of charge during 1-CCA-H- ozonolysis compared to 3- CCA-H- ozonolysis as shown in Figure 3.4.

The pseudo-first order reaction rates for both the reactions are given by the gradient of the exponential functions in Figure 3.4. The upper limits of the second rate order for both the reactions are calculated by taking the ratio of the pseudo-first order rate constant and the ozone concentration inside the ion-trap. The pseudo-first order and the upper limits for the second order rate constants for 1- and 3-CCA-H- ozonolysis are given in Table 3.1.

100 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

Table 3.1 Rate constants measured for the ozonolysis of 1 & 3-CCA in the modified ion-trap mass spectrometer at 307 K. Pseudo-first order values, k1, were calculated from the iodide/ozone reaction, the kinetics data is given in Appendix B. The reaction efficiencies are given in square brackets as a percentage of the calculated collision rate. a Reaction efficiencies based on theoretical collision rates calculated from a parameterized trajectory model.97 b Reaction of I- with ozone was carried out before running the samples to determine the ozone concentrations. c The second order rate constant for the reaction of the iodide ion with ozone was obtained from Williams et al.27

-1 -12 3 -1 -1 a Compound k1=k2[O3] (s ) k2 (× 10 cm molecule s ) [ф%] [1-CCA-H]- 1.99 ± 0.06 75.3 ± 3.2 [8.8] [3-CCA-H]- 0.16 ± 0.006 6.1 ± 2.4 [0.7] I- 0.264 ± 0.005b 10 ± 0.25c

The rate of ozonolysis for 1-CCA-H- is about 12.5 times faster than that for the 3-isomer based on the pseudo-first order reaction rates. Using the parametrized trajectory model of Su and Chesnavich, the collision rate was calculated between ozone and an ionic molecule with a mass of 125 atomic mass units. The collision rate was determined to be 8.55 × 10-10 molecule-1 cm3 s-1. The ratio of the second order rate constant and the collision rate gives the reaction efficiency (Φ). The calculated reaction efficiencies are also given in Table 3.1. The calculated reaction efficiency for the reaction between ozone and 1-CCA-H- is 8.8% and for the reaction between ozone and 3-CCA-H- is 0.7%. These quantitative rate data shows that although the reaction between these ions and ozone is intrinsically slow, the reaction efficiencies can be improved by more than 12 times just by changing the position of the double bond on the ion.

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 101

3.3.4 Explanation for the enhanced reaction rates

Ozonolysis is a 1,3-dipolar cycloaddition reaction; since the ozone is a 1,3 dipole it is regarded as an electrophile. The 1-CCA-H- ion comprises of 3 sp2 carbons, involved in π-bonds; the C=C bond between carbon 1 and 2 and the carboxylic C=O bond. Although the isomer 3-CCA-H- also comprises of the same number of electrons involved in the same π bonds, the vinyl carbons are 3 carbons away from the carboxylic head group. This reduces the nucleophilic character of the C=C for the 3-CCA-H- possibly due to the absence of π conjugation between the C=C and C=O bonds. Sidebottom et al., have shown that substituting a hydrogen atom at the site of the double bond for cyclopentene and cyclohexene with a methyl group enhances ozonolysis reaction rates.143 The presence of the electron-donating group enhances the reactivity with the ozone. Thus, the location of the double bond with respect to the carboxylate head group affects reactivity of the ozone.

3.3.5 Rationalisation of products observed experimentally

Ozonolysis of 1-CCA-H- ions yielded major products with m/z 60, 139 and 141. The production of these ions is thought to occur via the mechanism shown in scheme 3.3. Addition of ozone via the Criegee mechanism produces the primary ozonide and subsequently, the O-O bond breaks resulting in a diradical ion. Since the O-O bond homolysis is exothermic in nature, the intermediate is formed with excess energy. This energy is either quenched by collisions with other molecules or is retained within the molecule. The tethered peroxyl radical is then able to interact with the carboxylate moiety resulting in the expulsion of a carbonate distonic ion •- (CO3 ) and a neutral radical product. Previously, Ly et al. have demonstrated that in the gas phase, reaction of α-carboxylate radical anions reacts with dioxygen to yield carbonate radical anions.144 In their study, the peroxyl radical product was formed from the reaction of acetate radical anions and dioxygen. The resulting acetate peroxyl radical has a similar structure to the Criegee diradical ion shown in Scheme 3.2; the presence of α-carboxylate peroxyl radical. They calculated that at the G3SX level of theory, the formation of the carbonate radical anion from the reaction between acetate radical anions and dioxygen is exothermic by 83.3 kcal mol-1 and the TS for the formation of these products sits -35.9 kcal mol-1 below the entrance channel. Given that POZ formation step is exothermic by 60 kcal mol-1 for the

102 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

charged ion and ozone reaction, the TS for the formation of the carbonate ion is thus thermodynamically and kinetically feasible.

Scheme 3.3: Suggested reaction mechanism for the formation of the m/z 139 and m/z 60 ion during the ozonolysis of the 1-CCA-H- ion.

The tethered peroxyl radical intermediate can also participate in a 1-4 hydrogen shift reaction resulting in a charged product with carbonyl and groups although 1-4 hydrogen shifts are not common.145 The resultant loss of the then results in an endocyclic alkene with m/z 139 which can possibly further participate in secondary ozonolysis reactions. Hydrogen peroxide is a known product in ozonolysis reactions and its formation rates are enhanced under humid conditions. For instance, hydrogen peroxide yields range from 1 – 9 % for dry and humid conditions respectively from isoprene ozonolysis.146

The m/z 141 ion is thought to be an epoxide ion where one oxygen atom is incorporated into the olefin ion, resulting in an epoxide ion and molecular oxygen. As mentioned in the introduction, epoxide formation does not comply with the Criegee mechanism of ozonolysis; instead, it is known to be a “partial cleavage” product. Cremer and Bock147 have suggested upon reviewing compelling experimental evidence that the Criegee intermediate can participate in epoxidation reactions. However, in the ozonolysis of cyclic alkenes, the Criegee intermediate (CI) and the carbonyl fragment are tethered together and it is imperative that the CI retains all the nascent energy. It is predicted that for cyclohexenes, the total yield for stable Criegee intermediates is negligible.148 Anglada et al., describe a concerted

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 103

mechanism for the formation of an epoxide and an excited oxygen molecule from a diradical intermediate produced from POZ decomposition during ethylene ozonolysis.127 The diradical intermediate when formed is likely to have a range of rotational isomers due to the rotation about the C-C bond. However, in the case of 1- CCA-H- ozonolysis, the diradical intermediate product has restricted rotational mobility due to the cyclic nature of the product. Although it is difficult to prove the exact mechanism for epoxidation, it is generally accepted that +16 Da additions to an 149 alkene during ozonolysis is through epoxidation by O3. The importance of epoxides in the atmosphere has been highlighted recently as a precursor to SOA formation.150–152

3.4 Computational studies of cyclohexene carboxylic acid and cyhohexene carboxylate ozonolysis

3.4.1 Charge loss processes

In the experiments described above no ionic product is observed that correlates with depletion of the reagent ion, i.e., a loss of ion count signal was observed. This is attributed to an ozonolysis reaction resulting in either neutral products and an unbound electron or low mass ions that are inefficiently captured and detected by the ion-trap instrument. Electron loss processes from negative ions can occur through an expulsion of an electron from an energised negative ion and can arise when the exothermicity of a gas phase reaction exceeds the electron binding energy of the anion. Also, it can occur through a collision between a negative ion and a neutral compound (associative detachment).153 The process of ozonolysis is extremely “hot” with formation of the ozonide itself depositing up to 60 kcal mol-1 that could facilitate prompt ejection of an electron. One possible pathway for electron ejection in the reaction of 1-CCA-H- with ozone is outlined in Scheme 3.2. In this scheme, a diradical aldehyde anion formed during ozonolysis could rearrange to form a vinyl hydroperoxide. Subsequent loss of a hydroxide radical could form a distonic ion. Following this, a hydrogen shift could occur resulting in an expulsion of an electron and the formation of a neutral compound which is not detected.

104 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

O O O- - - O - OH O O O O O O O O O H-Shift Ozonolysis O O O O O O O O

m/z 125 -OH

O- OHO O O e- O O O H-Shift

Scheme 3.2: An example of a charge loss process starting from a primary ozonide.

Figure 3.6: The potential energy surface depicting the energetics of charge loss process outlined in Scheme 3.2.

The prompt dissociation of the C-C and one of the O-O bonds in the primary ozonide leads to an energetic diradical compound. The energy can be internalised through intramolecular rearrangements such as hydrogen atom shifts. Such processes could eventually be a source of an electron as the charge molecule is converted into a

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 105

neutral. The potential energy surface in Figure 3.6 gives evidence of this possibility. Since ozonolysis is exothermic by about 60 kcal mol-1, this could provide an energy for an ejection of a hydroxyl radical as shown in Figure 3.6.

3.4.2 Potential energy surface for 1- and 3-cyclohexene carboxylate and carboxylic acid ozonolysis

The potential energy surface for alkene ozonolysis has previously been investigated both theoretically and experimentally. In the first step of Criegee ozonolysis, the ozone adds to the alkene with a low barrier (~5 kcal mol-1) forming a primary ozonide. Ozonide formation is exothermic and releases ~60 kcal mol-1 of energy. The experimental activation energy for the Criegee addition of ozone to cyclohexene is ~2.1 kcal mol-1 and the calculated value is 1.3 kcal mol-1 at the B3LYP/6-31G(d) level of theory.154

Figure 3.7: Zero-point corrected PES for the O3 – 1-CCA (neutral, black) and 1- CCA-H- (charged, red) reaction (syn pathway for Criegee mechanism) calculated at the B3LYP/6-31+G(d,p) level of theory. The prefix D and C represents DeMore and the Criegee pathways with D1 and C1 representing the reaction pathway for the

106 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

neutral 1-CCA and ozone reaction and D2 and C2 representing reaction pathway for the 1-CCA-H- and ozone reaction. PreC, TS, Prod and SOZ refer to the pre-reactive complex, transition state, products and secondary ozonide, respectively.

Two different pathways, the Criegee mechanism and the DeMore mechanism are represented in Figure 3.7 by the PES for both sets of reactions. The neutral 1- CCA forms a pre-reactive complex with ozone and subsequently abstracting an oxygen, passing through a transistion state (TSD1) via the DeMore meachanism. 1 From TSD1, an epoxide and a singlet oxygen complex is formed, Prod (D2 + O2). The complex sits at -34.3 kcal mol-1 below the entrance channel.

The reaction between neutral 1-CCA and ozone also results in a pre-reactive complex (PreCC1). In this mechanism, the one of the terminal oxygen atoms in ozone approaches the vinylic carbon of the neutral 1-CCA forming a transition state (TSC1).

From this transition state, the primary ozonide is formed (ProdC1). The formation of the primary ozonide is exothermic by 54.3 kcal mol-1. The calculated activation energies for the formation of the primary ozonide from this reaction is 0.5 kcal mol-1 while the activation energy required for the formation of the DeMore pathway 1 -1 products (Prod (D1 + O2)) is 6.4 kcal mol .

Figure 3.7 also shows the PES of the reaction between 1-CCA anion with ozone, highlighting both the Criegee and DeMore pathways. In this case, the 1 formation of the epoxide and O2 produced via the DeMore mechanism is barrierless. This also applies to the formation of the primary ozonide produced via the Criegee mechanism. Both the pre-reactive complex formed via these mechanisms have similar calculated energies. The calculated energies for the transition states (TSD2 and

TSC2) for the DeMore and Criegee mechanism respectively are below the entrance channel. The calculated energy for the TSC2 via the Criegee mechanism is lower by about 2 kcal mol-1. The PES shows that the formation of the primary ozonide is exothermic by 62.6 kcal mol-1. This energy is about 8 kcal mol-1 lower compared to the exothermicity for the formation of the epoxide and singlet oxygen via the DeMore mechanism.

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 107

Also, included in the PES is the secondary ozonide (SOZ) which is formed from the interaction between the carbonyl and the carbonyl oxide products resulting from the breaking of O-O and C-C bonds in the primary ozonide. This product sits deeper at about 103 kcal mol-1 for the charged compound ozonolysis and 98 kcal mol- 1 for the neutral compound ozonolysis. For comparison, the SOZ for cyclohexene ozonolysis sits at 102 kcal mol-1 and for cyclopropene ozonolysis the SOZ is at 101 kcal mol-1 below the entrance channel.29,155 These calculations were derived from the B3LYP/6-31G(d) and the accurate CBS-QB3 levels of theory respectively.

Figure 3.8 shows the similar PES for the reaction between ozone and both the neutral 3-CCA and the 3-CCA anion. The reactions via both the DeMore and Criegee pathways are barrier-less for the reaction between ozone and the ion. However, the DeMore pathway for the reaction between ozone and the neutral 3-CCA results in a -1 transition state (TSD3) which sits energetically 13.7 kcal mol above the entrance channel. The calculated energies for the product formation via both the pathways are similar compared to the PES shown in Figure 3.7. The calculations show that the reaction between isomeric CCA ions and ozone via the different mechanism are both kinetically and thermodynamically favoured; that there are no barriers to the formation of the reaction products.

108 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

Figure 3.8: Zero-point corrected PES for the O3 + 3-CCA (neutral, black) and 3- CCA-H- (charged, red) reaction (syn pathway for Criegee mechanism) calculated at the B3LYP/6-31+G(d,p) level of theory. The prefix D and C represents DeMore and the Criegee pathways with D3 and C3 representing the reaction pathway for the neutral 3-CCA and ozone reaction and D3 and C3 representing reaction pathway the 3-CCA-H- and ozone reaction. PreC, TS Prod and SOZ refers to the pre-reactive complex, transition state, products and secondary ozonide respectively.

The calculated reaction efficiencies for the reaction of the isomeric ions with ozone are given in Table 3.1. The calculated reaction efficiency is 8.8% and 0.7% for

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 109

the reaction between 1-CCA-H- and 3-CCA-H- with ozone respectively. Firstly, given the strong oxidizing properties of ozone and secondly, the calculated, barrier- less and exothermic formation of the products from the reaction of ozone with both isomeric ions imply that the reaction should proceed efficiently. However, it is surprising that the reactive efficiencies are low.

There are examples in the literature where this seems to be generally true for the reaction of molecular ions and ozone. For instance, Pham et al., have shown that the gas phase ozonolysis reaction of fatty acid methyl ester ions with ozone are inefficient under similar conditions.132 In their experiments, the fatty acid methyl esters carried a positive charge due to adducting ions such as Li, Na and K. These positive ions were then subjected to same ion-trapping ozonolysis experiments. They also showed that the nature of the adducting positive ion with the fatty acid methyl ester has a profound effect on the reaction rate constant and the reaction efficiencies. The fastest reaction rate was calculated when the adducting ion was Li followed by Na and finally K. This implies that while having the charge is necessary for these trapping experiments to work, the nature of charge contributor is important in these reactions. Not only is the ozone molecule active towards the site of the double bond, the charge and the nature of the charge seems to affect how quickly ozone reacts with the ion.

The reaction efficiency is a function of both the reaction rate and the collision rates. The reaction efficiency is calculated to be a small number because the determined reaction rate is much smaller than the calculated collision rate. The Arrhenius equation shows that the reaction rate is dependent on both the pre- exponential factor as well as the activation energy. The calculated PES shows that the activation energies for the ozonolysis reactions of these isomeric ions are low. While this implies that the probability that the ion-neutral collision resulting in a reaction forming ozonolysis products is high, the measured reaction rate suggests otherwise. Therefore, one possible explanation for the low reaction rates is the assumed low pre-exponential factors for the reactions between molecular ions and ozone. This implies that the transition state for the formation of primary ozonide is highly ordered. Given this constraint, the number of successful collision resulting in the formation of ozonolysis products is reduced. It has been suggested that the

110 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

differences in the ring-strain energies of cyclohexenes affects the rate constants for the reaction of ozone with cyclohexenes.143 However, in our case, the ring-strain energies should be similar for both the CCA isomer ions.

Although the relative differences in the reaction rates between the 1-CCA and 3- CCA ions with ozone can be explained by the position of the double bond relative to the charged head group, the overall low reaction efficiencies is thought to be largely related to variations in the pre-exponential factors given the similar activation energies calculated at the B3LYP/6-31+G(d,p) level of theory.

3.4.3 TS geometries for the ozonolysis of 1-cyclohexene-1-carboxylic acid and 1- cyclohexene-1-carboxylate

The computed geometric properties are comparable to structures obtained in the literature.7,8,16 The comparison of the TS geometry for the ozonolysis of 1-CCA and 1-CCA-H- via the Criegee and the DeMore mechanism is shown in Figure 3.9. The TS geometry (Figure 3.7 (a)) for the 1-CCA ozonolysis via the Criegee mechanism shows that the C-O bonds are 2.32 and 2.40 Å. These bonds are slightly longer than those obtained from ethylene ozonolysis at the CASSCF level (2.113 Å) and the MP2 level (2.164 Å).127,156 The vinylic carbons in ethylene are secondary in nature but for 1-CCA and 1-CCA-H-, they are tertiary in nature. The absence of extra bonded to the vinyl carbons could be the reason for the elongation of the C-O bond due to steric hindrance. Also, the interaction between the proton at the carboxylic acid head group and the ozone could mean that the ozone molecule is closer to the vinylic carbons. The C-O bond length for the TS of the charged 1-CCA-H- is longer still by about 0.07 Å. This is probably due the presence of the charged repulsive carboxylate group. There are little differences in the bond lengths of the vinylic carbons in this case.

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 111

Figure 3.9: TS geometry for ozone-neutral (1-CCA) and ozone-ion(1-CCA-H-) complex for the Criegee (a,b) and the DeMore (c,d) mechanisms.

For the geometry representing the DeMore mechanism (3.7 (c) and (d)), the C=C bonds are slightly longer, 1.41 and 1.40 Å, respectively, for 1-CCA and 1- CCA-H-. For the 1-CCA case, the C-O bond length is less than that for the 1-CCA-H- , 1.81 Å for 1-CCA and 1.89 Å for 1-CCA-H-. The interaction of the carboxylic proton with central oxygen atom in ozone could be the reason for the difference in the C-O bond lengths.

Figure 3.10: TS geometry for ozone-neutral (1-CCA) and ozone-ion (1-CCA-H-) complex for the Criegee (a,b) and the DeMore (c,d) mechanisms.

112 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

Figure 3.10 shows the comparison for the TS geometry for the 3-CCA+ozone (a,b) and 3-CCA-H-+ozone (c,d) complexes. The trends that were observed in Figure 3.7 are also mirrored in this figure. Again, the C-O bond length is longer for the charged ion-ozone TS structure representing the Criegee mechanism compared to the neutral-ozone TS structure (2.38 and 2.33 Å vs 2.49 and 2.42 Å). However, the C-O bond elongation for the neutral-ozone TS case cannot be explained by the interaction of the carboxylic proton and the ozone molecule. The interaction between the ozone molecule and the cyclohexene ring is a more reasonable explanation. For the TS representing the DeMore mechanism, the trends are also conserved as in Figure 5. The C-O bond is longer for the charged-ozone TS complex than the neutral-ozone TS complex. Also, the C=C bond is slightly longer at 1.40 Å compared to 1.37 Å for the 3-CCA+ozone and 3-CCA-H-+ozone complexes, respectively.

As the potential energy surface was explored for the reaction between 1- CCA-H- and ozone via the DeMore mechanism, a minimum energy product with a β -lactone moiety in its structure was fortuitously obtained in the calculations (Figure 3.11). To investigate if the m/z 141 ion observed could be a lactone instead of an epoxide, the PES of the ozonolysis of the propanoate anion as a surrogate compound at the same level of theory and basis set was calculated and explored.

Figure 3.11: The isomeric structures of the epoxide and the β-lactone.

The PES of the ozonolysis of propenoate anion (Figure 3.11) shows that the formation of the epoxide and the singlet molecular oxygen is exothermic by about 30 kcal mol-1. The other pathway involves the formation of the POZ though the Criegee pathway releasing about 62 kcal mol-1 of energy. Instead of O-O bond homolysis, the charged oxygen attacks the β-carbon of the POZ, resulting in a formation of a β- lactone with a barrier of 30 kcal mol-1. The resulting 4-membered β-lactone and

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 113

singlet molecule resides at 19.6 kcal mol-1 relative to the entrance channel. Although this sits about 16 kcal mol-1 above the epoxide and molecular oxygen formed from the DeMore channel, the barrier to its formation is still thermodynamically accessible.

Scheme 3.4: Formation of a (a) β-lactone from the primary ozonide derived from the ozonolysis of propenoate ion. (b) Charge induced formation of an epoxide from an α- lactone also derived from the primary ozonide from the propenoate ion and ozone reaction.

Traditionally, the fate for the POZ has been the subsequent decomposition into the Criegee intermediate and a carbonyl compound. However, it was shown that the presence of a charge can lead to an epoxide formation without adhering to the DeMore mechanism and also to a β-lactone from the POZ though a charged induced unimolecular process.

114 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

Figure 3.12: The PES of propenoate ion ozonolysis. The formation of the epoxide and β-lactone from the POZ is shown separately to highlight the different processes.

3.5 Conclusion and atmospheric implications

Ozonolysis of charged 1-and 3-cyclohexene carboxylates within a modified ion-trap spectrometer showed remarkable differences in the reaction rates and efficiencies between the isomers. Quantum calculations show that the POZ formation is exothermic by ~60 kcal mol-1 consistent with the exothermicity of neutral ozonolysis reactions. The charge can have a profound effect on the formation of unique products such as α-lactones which can result in the formation of epoxides without invoking the DeMore mechanism. However, the DeMore mechanism cannot be entirely excluded to rationalise the formation of the m/z 141 ion. Furthermore, it is inferred that the formation of the m/z 60 ion that at least the first step of the Criegee mechanism must be occurring.

The implication of the research presented in this chapter can be derived from -1 the comparison of the atmospheric lifetimes (where lifetime s = 1/Kx[O3]) of the ions with respect to removal by ozone in the troposphere.

While there are no reported values for the reaction rate constants of the reaction between the neutral 1- and 3-CCA with ozone, the second order rate

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 115

constants of the reactions of cyclohexene with ozone have been published. The second order rate constant for the reaction of cyclohexene with ozone is 81.4 × 10-18 cm3 molecule-1 s-1.157 This value is lower than what was obtained for the reaction between the cyclohexene carboxylate anion isomers by a factor of 6.

Given the typical ozone concentrations in polluted environments of 40 ppb 10 -3 (corresponding to 2.64 × 10 molecule cm O3), the atmospheric lifetimes of these gas phase ions in the presence of ozone can be estimated. The half-life of 1- and 3- CCA is calculated to be 0.5 s and 6.2 s respectively. However, the neutral cyclohexene has a calculated lifetime of 4.7 × 105 s. This implies that the ions are oxidized in such environments rapidly and do not accumulate in the troposphere. Furthermore, it has been reported that the magnitude of removal of cycloalkenes by 143 OH and NO3 is similar to the removal by O3. If this is also true for the removal of these alkene ions by these oxidants, the removal of such ions in the atmosphere by ozone is important.

The removal of biogenic terpenes has been shown to be efficient sources of secondary aerosols. If the charged analogue of these alkenes show similar enhanced reactivity compared to the neutral compounds, the rapid removal of these compounds could be an important sources of secondary organic aerosol precursors.

116 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

Chapter 4: Reaction of iodide and bromide ions with ozone in the gas phase

4.1 Introduction

Ozone is the largest source of the OH radical which is an important scavenger for trace gases in the atmosphere.1 Processes which affects the concentration of ozone affect the oxidative capacity of the troposphere. The reduction of tropospheric ozone has implications in both the climate perturbation and understanding its formation and destruction processes is vital in constraining global ozone budgets.158

The formation of reactive halogen oxides such as bromide and iodide oxides are thought to originate from sea salt aerosol spray and marine algae sources respectively. In the polar boundary layer, bromide explosion events are marked with enhanced depletion of tropospheric ozone.159–161 The heterogeneous reaction between Br-, which is concentrated in a thin layer on the surface of ice (quasi-liquid layer, QLL), and gaseous ozone has been suggested to form bromine gas in the presence of protons.162–164 Subsequently, the degassed bromine gas is broken down via photolysis forming bromine atoms which then react with ozone forming bromine oxides. In non-acidic interfaces, the production of molecular bromine has been suggested via a - 165 charge transfer mechanism from O3 .

Although the concentration of iodine compounds in the ocean is too small to account for the observed iodine oxide concentrations, reactive iodine (I and IO) is expected to have an impact on the polar boundary ozone concentration.159,166 The production of iodocarbons by marine algae and is thought to involve several enzymatic processes and the haloform reaction.167,168 These volatile compounds have low and are subsequently degassed into the atmosphere and are broken down by sunlight forming active iodine.

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 117

Even though there is compelling evidence that ozone reacts with halide ions (I- and Br-) at air-surface interfaces, in frozen solutions or when marine aerosol is deposited in the snowpack, how this occurs exactly is still debatable.165,169–172 Probing interfacial chemistry is often complicated while fundamental gas phase studies lift many of these constraints and direct experimental investigation is possible. Williams et al. determined the second order rate constant for the reaction between the Iodide ion and ozone in the gas phase to be 1.0 ± 0.25 × 10 -11 cm3 -1 77 molecule s . Using a selected-ion flow tube, the authors did not observe any other product channels other than the clustering of ozone with I- ions. In the solution phase, studies of the oxidation of halide ions by ozone are extensive. A common feature of such reactions indicates a step-wise oxidation mechanism for halide ions. - An O-atom transfer from ozone to the halide ion via a halide-O3 intermediate is thought to be much more important than an electron transfer mechanism producing - 173 Br atoms and O3 in the solution phase.

+ → + (4.1)

+ → + (4.2)

+ → + (4.3)

However, there are very few studies of such reactions in the gas phase. Obtaining the reaction rate constants for these reactions (4.1 - 4.3) and the verification of the reaction mechanism will supplement and aid in the study of these reactions in the solution phase as well as in the quasi liquid layer.

Recently, Gladich et al., explored the potential energy surface of the bromide ion with ozone ((Reaction (4.1)) using a high level ab initio theory.174 The authors highlight a previously unknown surface crossing mechanism for the formation of bromite ions. This surface hopping mechanism could be conserved for the neutral ions as well and may be important as bromine oxides have been found in the Artic snowpack prior to the polar sunrise.163

118 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

In this chapter of the dissertation, a systematic experimental study of the reactions of bromide and iodide ions with ozone is presented. A modified ion-trap mass spectrometer which allows the inclusion of ozone gas within the ion-trap as described in Chapter 2 of this thesis is utilised. Once the precursor ions are mass selected, the kinetic studies of the ions are carried out by varying the trapping time of the halide ions in the ion-trap in the presence of ozone. The potential energy surfaces - of the reaction between BrO + O3 is also explored using the starting point ab initio calibration method suggested by Gladich et al. This work builds upon their results for a more complete understanding of halide ion oxidation in the gas phase.

4.2 Methods

4.2.1 Instrumentation

Experiments were conducted on a linear ion-trap mass spectrometer (LTQ, Thermo Fisher Scientific, San Jose, CA, USA) that has been modified to allow ozone gas to enter the ion-trapping region. To generate [M-H]- halide anions, potassium iodide and 4-(bromomethyl )benzoic acid (Sigma-Aldrich, St. Louis, USA) were dissolved in methanol (ca. 50 μM) and infused into the electrospray ionization source of the instrument with a flow rate of 10 μL min-1. The instrument was operated in negative ion mode using a spray voltage of 5 kV; a capillary voltage of 27 V; a tube lens voltage of 170 V; and the temperature of the heated transfer-capillary was set to 275 °C. For ion-source ozonolysis experiments, the spray voltage used was between 3 – 8 kV and oxygen ((99.99%, Coregas, Yennora, AUS) was used as the nebulising gas.101

For tandem mass spectrometry experiments ions were mass-selected using an isolation width of between 1 and 5 Th. For collision-induced dissociation selected ions were subjected to a normalised collision energy of between 15 and 30 (arbitrary units) for an activation time of 30 ms. For gas phase ion-molecule reactions normalised collision energy was set to 0 and activation times of between 30 and 10,000 ms were set representing the reaction time. For gas phase ozonolysis reactions, ozone was introduced into the flow of UHP helium (BOC gases, Cringila, AUS) via a gas-mixing manifold as previously described.175 Stated concentration of

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 119

ozone was generated from high purity oxygen gas (99.99%, Coregas, Yennora, AUS) using an ozone generator (HC-30, Ozone Solutions,Iowa, USA) and introduced to the helium flow using a chemically inert PEEKsil (SGE Analytical Science, Australia) tubing (100 mm, 25 µm I.D.). The concentration of ozone produced was -3 -3 240 g Nm (“High” O3) and 12 g/Nm (“Low” O3) which was measured using an ozone analyser (UV-106H, Ozone Solutions, Iowa, USA). The helium gas was supplied via a variable leak valve (Granville-Phillips, Boulder, CO, USA) to maintain an ion gauge pressure of ca. 0.70 x 10-5 Torr.

4.2.2 Computational method

All the calculations are performed using the Gaussian 09 program packages.136 The geometries of all the reactant, products, intermediates and transition states were optimized using the methods outlined by Gladich et al.174 Briefly, initial geometry optimisation for the reactants and transition state structures were done using the unrestricted MP2 level of theory using the 6-311+G(d,p) basis set. The geometries were then further refined at the UCCSD level of theory at the same basis set. Due to the multi-configurational nature of the transition state species, the potential energy surface may be further improved through the use of a multi- reference approach.140,141 However, these computationally intensive methods were not employed in the present study and may form the basis for future investigations.

Frequency calculations were performed at UCCSD level to check the obtained species is an intermediate (with all real frequencies) or a transition state (with one and only one imaginary frequency) and to characterize zero-point vibrational energy (ZPVE). To confirm the transition state connects designated intermediates, intrinsic reaction coordinate (IRC) calculations were performed at the UMP2/6-311+G(d,p) level of theory. Only the singlet surface was explored. The energies are given in kcal mol-1 and are zero point corrected. The Cartesian coordinates for the transition states are given in the appendix.

120 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

4.3 Results and Discussion

4.3.1 Iodide and ozone reactions

The modified mass spectrometer enables the entrapment of mass selected ions in the presence of neutral gases. As the ions are trapped for different reaction time, the kinetic and mechanistic information of the reaction between the ion and the neutral gas can be extracted. The reaction proceeds under pseudo-first order conditions as the reagent gas is in much higher concentration than the ions [He buffer gas ˃˃ Ozone gas >> Ions]. Ideally, in such experiments, a quantitative conversion of the reactant ion to a single or a few products can be readily observed with little or no additional background ions.

Negative mode electrospray ionization (ESI) of methanolic solution of potassium iodide yields abundant ions at m/z 127, the iodide ion. Isolation of the - iodide ion in the presence of ozone forms the iodiate, IO3 ions at m/z 175 (Figure 1(a) through (c)). This is consistent with the results of Williams et al., who observed the formation of the iodate ions SIFT instrument operating at a higher pressure (0.4 Torr vs 2.5 mTorr in our experiments).77

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 121

Figure 4.1: Negative mode MS spectra of KI solution: a) Full negative MS spectrum of methanolic solution of KI; b) 30 ms isolation of the m/z 127 ions in the ion-trap, the region between m/z 135 – 165 is magnified 50x to show the absence of any ions c) 10 s isolation of the m/z 127 ions in the ion-trap in the presence of ozone resulting in the formation of m/z 175 ions.

Subsequent isolation of the m/z 175 ion and irradiation by a pulse of Nd:YAG laser at 266 nm (4.66 eV) resulted in the formation of three different photoproducts, m/z 127, 143 and 159 ions corresponding to the iodide, hypo-iodite and iodite ions (Figure 2). This provided an unequivocal identity of the m/z 175 ion as being an iodate ion.

122 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

Figure 4.2: Photo-dissociation spectrum of the isolated m/z 175 peak produced in - reaction between I and O3 within the ion-trap.

Isolation of the iodide ions under the same ozone concentration but at increased reaction times resulted in the increase of the relative abundance of the iodate ions at the expense of the iodide ions. This transformation of peak abundances between these two peaks was translated into a kinetic plot as a function of reaction time. The exponential decay in the signal for the iodate ion was matched by a corresponding rise in the relative abundances of the iodate ions. The resulting ln plot of the kinetics of the reaction gave the pseudo-first order rate constant (Figure 4.3).

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 123

- - Figure 4.3: Kinetics of the I and O3 reaction. (a) The exponential decay of the I ion - counts is matched by the corresponding rise in the IO3 peaks. (b) Linear fit of the pseudo first order reaction. The equation of the fit, as well as the R2, value are given. The error bars represent 1σ of at least 50 different data points at the reaction time.

- The half-life for the reaction between I and O3 was calculated to be 2.54 s. The pseudo first order rate constant from Figure 4.3(b) is 0.276 ± 0.005 s-1. Using this and the literature value for the second order rate constant for the reaction which is 1.0 ± 0.25 x 10-11 cm3 molecule-1 s-1, the concentration of ozone in the ion-trap was determined to be 2.76 ± 0.83 x 1010 molecules cm3.77

Figure 4.4: The residual plot showing the deviations between the predicted and - observed data points in the linear fit of I + O3 reaction as given in Figure 4.3(b).

The data points for the ln plot (Figure 4.3(b)) meanders along the straight line fit. To highlight differences between the data points and the predicted values by the fitted equation, a residual plot was constructed (Figure 4.4). Although the R2

124 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

value of the ln plot implies an excellent fit, the linear regression line systematically under-predicts or over-predicts the data as shown in the residual plot. This provided - evidence that the reaction between I and O3 was not as straight forward as it seemed.

Upon closer inspection, the spectrum for the reaction of the iodide ions with ozone for 10 s shows additional peaks at m/z 143 and 159 corresponding to the hypo- iodite and the iodite ions (Figure 4.1(c)). Sequential isolation of these ions was not possible as they were formed in low relative abundances. Utilizing another approach, these ions were formed by ESI carried out under high potential voltages under the presence of oxygen gas instead of nitrogen gas as a nebulising gas.134 The resulting corona discharge produced ozone which then reacted with the iodide ion in situ rather than in vacuo producing both the hypo-iodite and iodite ions (termed in-source ozonolysis). It was then possible to mass select and subsequently trap these ions within the ion-trap infused with ozone gas to probe the kinetics of Reactions 4.2 and 4.3.

Isolation of the m/z 143 ion in the presence of ozone resulted in the formation of iodide, iodite and iodate ions (Figure 4.5(a)). It was postulated that the reaction between the hypo-iodite and ozone produced iodite and molecular oxygen. Following this, the rapid conversion of iodite to iodate ions was then possible. The kinetic data is given in Figure 4.6(a). The ln fit in the kinetic plot for the consumption of m/z 143 given in the Appendix (Figure B.1(b)) implies that the reaction is not pseudo-first order. However, assuming that it is the case and the upper limit for the reactions between the hypoiodite ion (IO-) with ozone is calculated to be 1.43 ± 0.066 × 108 cm3 molecule-1 s-1. This value is derived from the assumed pseudo first order value of 17.171 ± 0.787 s-1 and the ozone concentration of 1.20 ± 0.004 × 109 molecules cm-3. The concentration of ozone was obtained from the relationship of the external ozone concentration (12 g Nm-3) to the internal ozone concentration (Figure 2.12 in Chapter 2 of this dissertation).

The formation of the m/z 159 ion reaches a maximum and gradually falls while the formation of the m/z 175 ion increases quickly and gradually tapers off. An interesting aspect of this experimental result is the regeneration of I- ions. The production of I atoms in neutral gas phase studies has been attributed to the self-

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 125

reaction of iodine oxide radicals.176,177 Although we were not able to directly probe the self-reaction of IO-, the ion was isolated and trapped under the presence of oxygen. The reaction between IO- ion and molecular oxygen was slow, I- was formed with the other product possibly being O3. It was not possible for us to confirm that the other product was indeed ozone. This led us to conclude that the I- ion regenerated was as a result from the reaction between IO- ions and oxygen although the self-reaction between IO- ions cannot be ruled out.

- - Figure 4.5: Reaction of in-source produced IO and IO2 ions with ozone for 90 ms: - - (a) Reaction of the m/z 143 ion (IO ); (b) Reaction of the m/z 159 ion (IO2 ) with ozone for 90 ms.

Upon isolation of the m/z 159 ion, its conversion to the iodate ion in the presence of ozone was rapid even though the concentration of the ozone generated for this experiment was about twenty times lower than what was used for the reaction - -3 -3 between I and O3 (240 g Nm vs 12 g Nm O3) with the same He buffer gas dilution - (Figure 4.5(b)). The reaction kinetics observed for the reaction between I and O3 by Williams et al. was over a 2 ms reaction time and they did not observe the reaction - 77 between IO2 and O3. The kinetic data showed a pseudo-first order relationship between the concentration of ozone and the m/z 159 ions in the trap (Figure B.2(b) in

126 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

the Appendix). Therefore, the calculated upper limit for the second order rate - -8 3 constant for the reaction of iodite ion (IO2 ) with ozone is 1.95 ± 0.02 × 10 cm molecule-1 s-1. This value is about 2000 times the value for the gas phase oxidation of - - - - I ion to IO3 ! This rapid conversion of the IO2 to IO3 could be one of the reasons why the kinetics of this reaction has been elusive in the gas phase. The rate constant for this reaction has not yet been determined even in the solution phase. 178

- In the study of the BrO2 and O3 reaction in the solution phase, it was suggested that the presence of the BrO2 intermediate provided evidence of an - 173 electron transfer pathway producing the O3 ion. In this study, the presence of the - XO2 intermediate can be excluded as there is no evidence for the formation of the O3 ion (i.e. an ion at m/z 48 is not observed).

- - Figure 4.6: Kinetics of the reactions between O3 and IO (a) and IO2 (b) in the ion- trap.

Since both oxygen and ozone gas is introduced into the ion-trap, the reaction of these ions with oxygen must also be considered. Isolating the iodate ion in the presence of oxygen resulted in the production of the IO- ion (Figure 4.7(a)). This indicates a possible O-atom transfer to the oxygen atom. From Figure 4.5 (b), the forward step to form the hypoiodite ion occurs well within 90 ms, while in Figure 4.7(a), the reversible step occurs albeit slowly. After 5 s of reaction with oxygen, the m/z 127 is at 20% of the initial relative abundance. Thus, the hypoiodite forming step from I- and ozone occurs faster than the reversible step.

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 127

- - Figure 4.7: Reaction of in-source produced IO and IO2 ions with oxygen in the ion- - - trap for 5 s: a) Reaction of the m/z 143 ion (IO ); b) Reaction of the m/z 159 ion (IO2 ).

Trapping the iodite ion in the presence of oxygen for 5 s results in the formation of m/z 143 and m/z 127 ions as shown in Figure 4.7(b). Again, comparing - this result to the one obtained in Figure 4.5(b), this indicates that the iodite ion (IO2 ) formation step is also reversible. Also, the reversible step is slower based on the relative abundances of the m/z 159 peaks. In the forward step, the m/z 159 peak is already converted to m/z 175 to about 30% of its initial relative abundance; however, in the reverse step, after 5 s, the relative abundance of the m/z 143 peak is about 25%. This indicates a faster forward chemistry to form the iodate ion. However, trapping the iodate ion under the same conditions, failed to show any indication for - - the reversibility in the reaction for the formation of IO3 from IO2 and O3 (Figure 4.8).

128 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

- Figure 4.8: Reaction of in-source produced IO3 ions with oxygen in the ion-trap for 5 s.

In summary, probing the reactions involved in the oxidation of the iodite ion by ozone reveals step-wise chemistry involving key intermediates. The key reaction steps derived from the kinetic studies are summarised in Scheme 4.1. Although the - - reaction between IO and O3 which could potentially produce I and O2 is not included in the scheme, the reaction is a possibility and could not be excluded based on experimental evidence.

k1 - - I + O3 IO + O2 k1 >> k-1 k-1 k - 2 - IO + O3 IO2 + O2 k2 >> k-2 k-2

k3 IO - + O - 2 3 IO3 + O2 Scheme 4.1: The forward and reversible reactions with the representative reaction rate constants for the reaction between iodine containing ions with ozone and oxygen in the gas-phase.

4.3.2 Bromide and ozone reactions

ESI of a methanolic solution of 4-(Bromomethyl) benzoic acid in the negative mode yielded abundant [M-H]- ions at m/z 213 and 215. Collisional activation of

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 129

these ions yielded ions at m/z 79 and 81 respectively. Upon isolation of the 79Br- ion and trapping the ion in the presence of O3, additional ions at m/z 95, 113 and 127 were produced.

Figure 4.9: Production of m/z 79 ions and its subsequent reaction with ozone: a) The CID spectrum of m/z 213 ion resulting in the formation of the bromate ion amongst other CID products; b) Ions at m/z 95, 113 and 127 were formed when 79Br- was trapped with O3 for 10 s.

These ions are probably the bromite ion, BrO-, the bromite-water adduct ion, - - - BrO.H2O and the bromate ion, BrO3 . Apart from the BrO.H2O adduct ion, the - - production of BrO and BrO3 ions indicate similar chemistry occurring as iodide oxidation by ozone. The reaction of Br- ion with ozone was inherently too slow to determine an estimate of the pseudo-first order rate constant.

4.3.3 Computational results

4.3.3.1 Optimised geometry

The geometry of the reactants and products for reaction between ozone and Br-, - - BrO and BrO2 was calculated at the UCCSD/6-311+G(d,p) level of theory for both

130 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

the singlet and triplet states. The geometric parameters for the structures are given in 1 3 Table 4.1. The experimental data for the bond lengths and bond angles for O3, O2 and BrO- is also included and there is excellent agreement between the experimental 3 values and theory. The largest difference was for the bond length of O2 where the predicted value is smaller by 0.01Å. The Br-O bond distance for 3BrO- is greatly 3 - 3 - exaggerated compared to other Br-O bond distances for BrO2 and BrO3 . This interatomic distance is much larger than the experimentally derived Br-O bond distances.179 Table 4.1 Geometric parameters for the species at singlet and triplet surfaces calculated at the UCCSD/6-311+G(d,p) level of theory. Species Coordinate UCCSD/6- Experiment 311+G(d,p)

1 180 O3 r(O-O) 1.245 1.27276 ± 0.00015 θ(O-O-O) 118 116.7542 ± 0.0025180

1 O2 r(O-O) 1.205 1BrO- r(Br-O) 1.809 1.814 ± 0.009181

1 - BrO2 r(Br-O) 1.707 θ(O-Br-O) 111.8

1 - BrO3 r(Br-O) 1.628 θ(O-Br-O) 107 Dihedral θ(O-Br- -114.7 O-O)

3 O3 r(O-O) 1.283 θ(O-O-O) 129.1

3 182 O2 r(O-O) 1.198 1.2075 3BrO- r(Br-O) 2.575

3 - BrO2 r(Br-O) 1.805 θ(O-Br-O) 158.4

3 BrO3- r(Br-O) 1.649, 1.760 θ(O-Br-O) 106.1,147.7 Dihedral θ(O-Br- 180 O-O)

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 131

4.3.3.2 Transition state calculations

The transition state geometries were obtained at the UCCSD/6-311+G(d,p) level of theory and the cartesian coordinates of the optimised transition structures are - given in the Appendix section B.2. The transition state for the BrO and O3 reaction is given in Figure 4.10. The bond distance linking the two molecules, the BrO bond is 1.89Å. This is slightly longer than the experimental bond length of BrO- of 1.81Å. Likewise, one of the O-O bond lengths for the ozone molecule is longer at 1.41Å. Both the O-O bond distances are longer than what was obtained for the O-O ozone molecule which was 1.25Å. The O-O-O bond angle is also narrower than the expected 118○ which was obtained for the singlet ozone molecule at the UCCSD/6- 311+G(d,p) level. However, the O-Br-O bond angle is similar to the O-Br-O bond 1 - angle for BrO2 .

- The transition state for the BrO2 and O3 reaction shows an enlongated Br-O bond distance at 1.93Å. One of the O-O bond distance is also longer at 1.43Å. Again the O-O-O bond angle is narrower but the O-Br-O angle is similar to what is 1 - expected for the bond angle for BrO2 .

Figure 4.10: The singlet transition state structures for the reaction between BrO- and - O3 (left) and BrO2 and O3 (right). Interatomic distances in angstroms and bond angles are given.

4.3.3.3 Intrinsic reaction coordinate calculations

132 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

Intrinsic reaction coordinate (IRC) calculations were performed at the UMP2 level of theory using the 6-311+G(d,p) basis set to ensure that the transition states - - obtained for both the reactions between BrO and BrO2 with ozone, were connected to the corresponding reactants and the products. Figure 4.11 shows the IRC pathways for the reactions. The transition state structure is given at the 0th reaction coordinate and the relative energies for the structures are benchmarked against the energy of the transition state given in kJ mol-1.

Figure 4.11: The intrinsic reaction coordinate (IRC) pathways for the BrO- (left) and - BrO2 (right) reaction with ozone obtained at the UMP2 level of theory.

The IRC pathway for the BrO- and ozone reaction shows a double hump - profile which is different from the BrO2 and ozone reaction pathway. While there seems to be a seamless transition from the TS to the products in the reaction between - BrO2 and ozone, there seems to a bottleneck on the reaction surface for the reaction - - - between BrO and ozone. The BrO product has a planar geometry while the BrO2 ion is trigonal pyramidal.

4.3.3.4 Potential energy surface

- - The simplified potential energy surfaces (PES) for the BrO + O3 and BrO2 + O3 - reaction is given in Figure 4.12. A striking feature for the PES for the BrO2 + O3 reaction is that its products sit in a much deeper potential well than the products for - the BrO + O3 reaction.

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 133

- - Figure 4.12: The potential energy surfaces for the BrO + O3 (top) and BrO2 + O3 (bottom) reactions at the UCCSD\6-311+G(d,p) level of theory. Only the starting products, the transition state and the final products are shown. All species are in the singlet state and the energies are relative to the starting products for the reactions. The energies are reported in kcal mol-1.

- A direct comparison to the PES obtained from the Br + O3 by Gladich et al. could not be made since the singlet point energies at the UCCSD(T)/aug-cc-pVQZ were still being calculated.174 Apart from these computationally intensive - calculations, it can be seen from Figure 4.12 that the reaction forming BrO3 from - - BrO2 and ozone is more exothermic than the reaction forming BrO2 and a singlet oxygen. At the UCCSD\6-311+G(d,p) level of theory, the singlet-triplet gap for the oxygen molecule is 137 kJ mol-1. While these reactions were only explored on the singlet surface, the formation of the ground state triplet oxygen necessitates a singlet- triplet surface hopping mechanism. This means that the products will be lower still in energy by 137 kJ mol-1. However, it is unclear where exactly this surface hopping mechanism takes place along the surface. Gladich et al. suggest photoexcitation of singlet ozone to the triplet state to facilitate the exothermic reaction for the first step of bromide ozonolysis.174 However, Figure 4.12 shows that the subsequent oxidation steps are exothermic. This implies that the limiting step in the overall oxidation steps of the bromide ion is the first step; its conversion to BrO-. If this is true for the I- and ozone reactions as well, then, the kinetic data provides a consistent picture that the rate limiting step is the initial oxidation step.

134 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

4.4 Conclusion

4.4.1 Instrumentation

Previous measurement of the rate constants for the reaction between I- and ozone was determined using the selected-ion flow tube (SIFT) technique.183 In this method, selected ions of interests are introduced into the flow tube where it meets a steady flow of reactant gas. Different reaction ion products can be resolved from the reactants by utilizing a quadrupole at the end of the flow tube. In multi-stage, chemical reactions, ions which are produced initially during the reaction may participate in further chemistry within the flow tube. Therefore, the ability to mass- select such product ions in an ion trap mass spectrometer to probe subsequent chemistry is an important advantage and appropriate to investigate such reactions. These advantages have been shown to be paramount in understanding the multi-step reactions of I- with ozone.

The incorporation of the PEEKSIL tubing within the gas-mixing manifold allows for the control of ozone introduced into the ion trap. This represents another level of adjustment of practical ozone concentration utilized in the experiments. While the amount of ozone initially generated can be adjusted at the ozone generator, the concentration can be adjusted by varying the length of the PEEKSIL tube. The utility of such a control is that fast reactions occurring in the sub-millisecond timescales can be investigated using low concentrations of ozone gas. Williams et al. obtained a range of 2nd order rate constants for the reaction of ozone with various negative ions.183 The range of these reaction rates were between 10-9 – 10-13 molecule cm-3 s-1. With the extra dimension of control for ozone concentrations, the rate of rate constants determined using the set-up outlined was 10-8 – 10-12 molecules cm-3 s-1 (including the results from previous chapter). While the exact 2nd order rate constants - - nd could not be determined for the reactions between IO and IO2 , the 2 order rate constant upper limits were calculated to be in the order of 10-8 molecules cm-3 s-1. Therefore, the combined utility of monitoring secondary ion chemistry of reactive intermediates using a modified ion trap mass spectrometer and the ability to control the ozone concentration to a practical range provides a unique advantage when studying ozonolysis reactions of gas phase ions.

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 135

4.4.2 Experimental and theoretical results

- - The study of the ozonolysis reaction of I ion to produce the IO3 ion at 307 K revealed that sequential oxidation steps were involved. Each forward step incorporated an oxygen atom from ozone into the reacting ion, eventually resulting in - the formation of the IO3 product. The upper limits of the rate constants for the - reaction between IOx (x = 1, 2) and ozone were determined. Not only was the step- - wise mechanism unravelled, the reactions of IOx (x = 1, 2) with ozone was found to result in the reformation of the reactant ion. These results build on previous knowledge of gas phase ozonolysis of I- ions where a single-step gas phase chemistry was thought to occur. The reaction of the gas phase Br- ion with ozone also resulted in the production of similar oxidation products. However, the reaction of Br- and ozone was found to occur at a much slower rate and product ions were not formed in sufficient amounts to enable the ion trapping experiments and interrogation of the secondary chemistry.

High level coupled-cluster calculations at the UCCSD/6-311+G(d,p) level of theory were carried out to investigate the product channels for the reaction between - - - the ions BrO and BrO2 , with ozone. These systems were chosen over the IOx and ozone system as the calculations were less computationally intensive (i.e., the I- ion consists of 18 more electrons than the Br- ion and CCSD calculation convergence scale with the number N of electrons as N6) and it was assumed that the potential energy surface should be similar based on similar oxidation products observed in experiments.

A conclusive link between experiment and theory could not be made due to nd - - the lack of 2 order kinetic measurements for the BrO + O3 and BrO2 + O3 systems, as well as the lack of collision rate efficiency data. The calculated PES on the singlet 1 - 1 1 - 1 surface shows that the formation of the products BrO2 and O2 from BrO + O3 proceeds via a transition state which is about 8 kcal mol-1 lower in energy compared 1 - 1 1 - the transition state which results in the formation of BrO3 and O2 from BrO2 and 1 1 - 1 -1 O3. However, the products BrO3 and O2 sit at a deeper well at -140.4 kcal mol - 1 compared to the products from the other channel. The products from the BrO + O3

136 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

reaction channel is found at 30.2 kcal mol-1 below the entrance channel. As this 1 - energy is more than the activation energy required for the formation of BrO3 and 1 1 - 1 O2, initial formation of the BrO2 and O2 is exothermic enough to surmount this 1 - barrier to produce the highly stable BrO3 product. Thus, the formation of this product is highly favourable which partly explains its abundance observed in the gas phase ozonolysis experiments.

Given the results from the computational studies of the Br- oxidation by ozone, the potential energy surface is expected to be similar for the ozonolysis of I-. The initial reaction of I- and ozone should be exothermic resulting in the initial - - - formation of IO and subsequently forming IO2 and IO3 . The energy released in each step is predicted be more than the activation energy required to surmount the - barrier for the next step in the reaction, until the stable IO3 is formed.

4.4.3 Atmospheric implications

Previously, the oxidation of bromide and iodide ions was thought to involve a single step chemistry in the gas phase.183 However, it has been shown in this chapter - - that it is not the case. For every reaction that produces, XO3 from X (X = Br and I) and ozone, three molecules of ozone are consumed. This is three times more than what was perceived to be lost in the gas phase.

In the polar regions, events are thought to occur during spring time which results in the formation of bromine compounds. It is thought that on certain surfaces of features like frost flowers, snowpack and new ice, Br2 and BrCl are formed and degassed into the gas phase. Upon release, these compounds kick start catalytic heterogenous cycling between the aerosol and gas phase.184 Rapid photolysis of these compounds produce atomic Br and Cl atoms which can then react with ozone to produce the halogen oxides. These halogen oxides are thought to subsequently react with HO2 forming hypohalous acids such as HOBr and HOCl. Also, cross- and self-reactions of halogen oxides regenerate the atomic Br and Cl atoms, reigniting the O3 loss processes. These halogen oxides also can react with

NO2 forming compounds such as BrONO2. Thus, the interaction of these halogen

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 137

oxides with different atmospheric species play a major role in regulating tropospheric ozone.

While the chemistry of halogen oxides in polar regions have been extensively researched, the reaction of halogen ions with ozone in the gas phase has received minimal attention. As shown in this work, the consumption of 3 molecules of ozone - - in the reaction of X with ozone produces a highly stable XO3 (X = I, Br) species. These sets of reactions are not considered in current chemical models of ozone depletion in the polar regions. The mixing ratios of ozone in polar regions during springtime is about 30 – 40 ppbV. During one such ozone depletion event, a reduction from 39.7 ppbV to 1 ppbV was observed over a period of 7 hours, overnight.185 Although, catalytic cycles are thought to occur which promotes the rapid consumption of ozone, the competition between halogen oxide ions, HO2 and 186 NO2 in the consumption of ozone has not been studied. If the halogen oxide ions are more efficient in capturing ozone then, these sequential reactions are essentially halogen and ozone sinks. Then not only is ozone consumed rapidly, it is also locked away as stable halogen oxides.

The effects of the reaction of gas phase halogen oxide ions formed from the ozonolysis of halogen ions in the modulation of local regions of ozone is yet to be researched. However, as shown in this chapter, the consumption of three times more ozone prompts an experimental study of such effects to be conducted. Ion-ozone reactions are thought to occur much rapidly than neutral-ozone reactions and perhaps this rapid chemistry coupled with the enhanced number of ozone loss may play a large part in affecting the ozone concentration in polar regions.

138 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

Chapter 5: Development of a charge-tagging approach for the characterisation of chemical intermediates in the formation of secondary aerosols from the ozonolysis of cyclohexenes

5.1 Introduction

Organic aerosols constitute a major fraction (> 50%) of total aerosol mass. Ozonolysis of biogenic hydrocarbons is an efficient source of organic aerosols.142 Although, many compounds in organic aerosols have been characterised, sufficient knowledge of the composition of aerosols is still severely lacking due to their extreme spatial and temporal variations. Furthermore, atmospheric concentrations of sample amounts are only typically a few micrograms per cubic meter.104 Aerosols have an overall net cooling effect on the atmosphere therefore affecting the energy balance of the Earth’s atmosphere which in turn influences climate change.15 Aerosol particles also affect health, continual exposure to these particles have been linked to increased mortality from respiratory and cardiovascular diseases.105,106 Newer methods which help to characterise these complex mixtures are actively sought. A method utilising real-time extraction is attractive for the analysis of such complex mixtures compared to the traditional ‘off-line’ methods.

Off-line methods usually comprise of a sampling, chromatographic separation and/or extraction and analysis aspects. Usually each of these steps takes place in the hours to days’ time scales and during such prolonged processes, the samples suffer from sample losses as well as unwanted secondary reactions on collected samples.107 Most atmospheric processes occur in the seconds or minute timescales and by

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 139

utilizing such methods; the unique chemical fingerprint is lost during sampling.

Recently, newer off-line methods have made the extraction and/or separation part of the analysis redundant. Desorption electrospray (DESI) has been successfully applied to the characterisation of aerosol collected on Teflon filters and liquid extraction surface analysis (LESA) for particle analysis on rotating drum impactor samples.187,188 These methods directly sample from the substrate surface and provide high time resolution.

Online methods such as aerosol mass spectrometry (AMS) provide near real- time, highly time-resolved aerosol composition data but the ionisation sources usually employed are thermal desorption/electron ionisation (TD/EI) or laser desorption ionisation (LDI).189,190 These sources result in extensive fragmentation of ions, making structure elucidation challenging. Furthermore, there are logistical and other resource dependent challenges in doing field sampling with the AMS instruments.

Extractive electrospray ionisation (EESI) is a direct online mass spectrometric analysis method for the analysis of organic aerosol first described by Cooks et al. 10 years ago.191 The method utilises a solvent spray which is positioned at an angle to an analyte spray which contains the analyte dissolved in a compatible solvent. During analysis, these sprays intersect facilitating solvent to solvent extraction. The resulting turbulent mixture is directed towards a mass spectrometer inlet where subsequently gas phase ions are formed. EESI has been applied for the analysis of complex mixtures and trace compound analysis such as pictogram quantities of explosives on human skin, the detection of melamine in milk and more recently, to the analysis of secondary organic aerosols (SOA) samples.109,192–194

Doezema et al. utilized EESI-MS to analyse the SOA produced from the ozonolysis of α-pinene.194 The mass spectra obtained using EESI-MS exhibited similarly to those obtained from traditional chemical ionisation processes. This provided further evidence that the extractive processes are occurring as the particles dissolve in the solvent spray. Horan et al. also utilized a variant of EESI to analyse both particle and gas phase analytes and arrived at similar conclusions regarding the

140 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

utility of the technique as well as the extraction process.195 Recently, Ballimore and Kalberer analysed tartaric, maleic and oleic acid aerosol particles using an EESI technique.109 Subsequent comparison of the mass spectra obtained from the online analysis of the products formed from the ozonolysis of oleic acid showed similar products as those obtained from off-line analysis.

In this part of the PhD project, a variation of an EESI source is described and utilized for the online analysis of laboratory generated aerosol particles from the ozonolysis of Limonene. Limonene is used as it is an excellent source of aerosols from ozonolysis reactions however it is not readily ionisable itself. Subsequently, this technique is tested on a model compound with a readily ionisable functional group (1-cyclohexene carboxylic acid, 1-CCA) to investigate the initial stages of the chemistry leading from gas phase to aerosols.

5.2 Methods

5.2.1 Aerosol generation and filter extract analysis

The overall schematic for the experimental set-up for the generation and analysis of aerosols is given in Figure 2.19. Aerosols were generated by injecting 50 µL of d-Limonene (97% purity, Sigma-Aldrich, Australia) in a Schott bottle (250 mL) though a 1.5 mm hole in its cap. For the 1-cyclohexene carboxylic acid (97% purity, Sigma-Aldrich, Australia) experiments, 500 uL of 0.15M of the analyte in methanol was injected. Two Swagelok fittings were installed into the cap to allow the delivery of ozone into the Schott bottle as well as to transport the aerosol particles once generated into the ESI source via a ¼’ Teflon line (Figure 5.2). Ozone was generated using an ozone generator from high purity oxygen (Coregas 4.0, Australia). 2 L min-1 of oxygen was delivered to the ozone generator (1000BT-12, Enaly, USA) though a series of flow meters (Key instruments, USA) which enabled the adjustment of the O2 flow into the ozone generator. Once the particles were generated, they were directed to an ozone monitor (Model 106, 2B Tech, USA) as well to a condensation particle counter (Model 3022, TSI, USA) where the particle

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 141

was counted. Ambient ozone was also actively monitored (Series 300, Aeroqual, New Zealand).

A 3-way valve allowed the aerosol flow to be directed towards a filter holder (LS-47, Adventec MFS Inc., Japan) where a 47 mm filter was used to sample the aerosol particles. When not sampling, the filter holder could be by-passed using the

3-way valve. These filters were extracted with 10 ml of 1:1 (ACN:H2O), sonicated for 10 minutes and subsequently filtered using 35 mm disc filters. The extracts were then analysed under negative mode MS using 1:1 (ACN:H2O) as the ESI spray solvent.

Figure 5.2: Panel (a) shows the installed aerosol line guide from the side of the ESI source. Panels (b) and (c) shows the side view of the ESI source showing the changes to its configuration before and after the installation of the aerosol line guide. Panel (d) and (e) shows the “Schott bottle” cap with the attached Swagelok fittings as well as the sample introduction hole.

142 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

Eventually the aerosol particles were analysed using EESI utilizing typical negative mode spray conditions of -3.8 kV, -25 capillary and -50 tube lens voltages. These values were selected based on the generation of optimum signal counts for the 1-CCA-H- ions. LTQ-XL mass spectrometer was used for the MS experiments and typical conditions of 30 collision energy using an isolation width of 1.2 and 30 ms activation time was employed for the collision induced dissociation experiments (CID). Advanced data dependent analysis was also used where data dependent tandem (MS/MS) experiments were carried out on the top 10 most intense ions detected during the primary scan event.

The exhaust from the ESI source led to an ozone scrubber to remove any excess ozone which can be introduced into the ESI source from the ¼’ aerosol line from the Schott bottle. The ozone scrubbing solution was made up of a reducing 110 agent, sodium thiosulfate (Na2S2O3) and potassium iodide (KI) in water. In solution, the ozone oxidises the iodide ions into I2 and the thiosulfate reduces the I2 back into the iodide ions (Equation 5.1 and 5.2). The reaction induced a colour change from a clear solution to a light brown solution and provides a visual cue for the reducing reaction. Darker colour indicates that the scrubber solution should be replaced with a fresh solution.

+2 + ⇋ + +2 (5.1)

2 + ⇋ +2 (5.2)

5.3 Results and discussion

A custom experimental set-up was constructed based on the designs of Gallimore and Kalberer.109 While the group built a custom housing on the same ESI source, the modification presented here is simpler. However, their implementation

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 143

provides a finer control over how the aerosol line is directed towards the methanol solvent spray. There is control in both the x- and y-direction as well as an angular control via an angle adjustment knob. The version described here only allows for a crude control for the aerosol line in the x-direction. While other groups have reported the results from EESI experiments for the ozonolysis of α-pinene, there are no other reports of utilising EESI for the extractive analysis of aerosol formed from limonene ozonolysis.194,195 Wolkoff and co-workers analysed online ozonolysis products of limonene ozonolysis but used a different method of ionisation (atmospheric sampling townsend discharge ionisation) and their mass scan range in their instrument was limited to m/z 90 – 250.196

The mass spectrum was continuously acquired as ozone was continually generated and supplied to the “Schott bottle” (‘reaction chamber’) prior to the injection of Limonene. When the limonene was injected, the mass spectrum exhibited a near-instantaneous change (Figure 5.3 (a) and (b)). Both gas and particles which were forming were clearly being transported to the ESI interface and were being extracted by the EESI process. The mass spectrum showed the typical clusters of peaks expected from aerosol samples (Figure 5.3 (b)). The spectrum showed peaks in three distinct groups; Group 1 (50 < m/z < 300), Group II (300 < m/z < 450) and Group III (450 < m/z < 600). These clusters of peaks have been referred to as, monomers, dimers and trimers respectively in the literature.111 These ions are assumed to be products from the limonene ozonolysis. However, there is experimental evidence that ions larger than m/z 500 could arise from the interactions between the oxidation products and the seed particles in which these particles 197 condense. The major peaks are separated by 14 (CH2) and 16 (O) Dalton differences and are indicative of an aerosol mass spectrum (Figure 5.4).

144 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

Figure 5.3: EESI (-) mass spectrum (a) before and (b) after the injection of limonene into the Schott bottle. The pictures correspond to different stages of the experiment before and after the addition of limonene in the presence of ozone in the bottle. Spectrum (b) also indicates three regions colour coded according to the groups of masses: Group 1 in blue (50 < m/z < 300), Group II in beige (300 < m/z < 450) and Group III in green (450 < m/z < 600). The mass range 450 – 1000 is magnified 10x to highlight the presence of Group III peaks.

The presence of a cloud forming inside the “Schott bottle” gave a visual indication of the formation of aerosols as limonene was injected into the Schott bottle in the presence of ozone (Pictures in Figure 5.3).

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5.3.1 Identification of abundant products of limonene ozonolysis

Figure 5.4: EESI (-) mass spectrum (a) before and (b) after the injection of limonene in the Schott bottle in the presence of ozone. Only the mass range m/z 50-300 is shown to highlight the Group 1 peaks.

Figure 5.4 shows the differences in the mass spectrum before and after the injection of limonene in the Schott bottle. While the M+H+ ion of limonene of m/z 137 has been observed using PTR-MS, in our study, in the negative mode, the parent ion of limonene is not observed .198 The abundant peaks in Figure 5.4(b) are mostly odd nominal masses indicating that they are primarily even electron anions comprising carbon, hydrogen and oxygen.

146 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

One of the peaks shown in in Figure 5.4(b) has the m/z ratio of 183. This is potentially a limonene ozonolysis product anion ([M-H]-) with the ion composition - 108 C10H15O3 . Possible products with this ion composition could be the anions of Limonoic acid (1) and 7-hydroxy Limonaldehyde (2) (Figure 5.5). Since, on-line methods do not have a chromatographic component; the aerosol mass spectrum reveals many product ion peaks. To achieve better understanding of the structure of the product ions, a tandem (MS/MS) technique is necessary for qualitative identification. However, ion-traps are only capable of unit resolution and a peak on the mass spectrum can be representative of many different isomers which cannot be distinguished from each other.

Figure 5.5: Anions of limonoic acid (1) and 7-hydroxy-limonaldehyde (2) have been detected in the (-) mass spectrometric analysis of limonene ozonolysis samples.

Advanced data dependent analysis was utilised where data dependent tandem (MS/MS) experiments were carried out on the top 10 most intense ions detected during the primary scan event. This enabled the automation of CID experiments for the top 10 most intense ions after the initial full MS scan event, throughout the experiment. The automation simplified data collection and this data dependent approach had not been carried out by other groups.

The CID spectrum of m/z 183 shows the neutral fragments of 18 (H2O) and

44 (CO2) Da losses which is consistent for a carbonyl compound (Figure 5.6). These losses were also evident in the CID spectra of m/z 155, 169 and 197. These peaks exhibiting those characteristic losses are also separated by 14 Da with respect to each other. Therefore, these abundant ions in the Group 1 region of the limonene mass spectrum are indicative of having at least one carboxylic acid functionality in their structure. These ions are absent or much reduced in the absence of limonene in the Schott bottle. Carbonyls in general have been shown to have high ozone forming potential in polluted environments.199 However, they have high vapour pressures and

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 147

their formation cannot explain the production of organic aerosols from limonene ozonolysis. Carboxylic acids on the other hand due to their high polarity and low vapour pressures, have been suggested to play an important role in the formation of SOA.200,201 However, there is also evidence that CIs also play an important role in the particle formation.202

Figure 5.6: Panels a – f shows the mass spectrum of the CID (MS2) fragments of the precursor ions shown. Certain areas are magnified to highlight ions with low abundances.

Limonoic acid was found to be a major ozonolysis product from limonene ozonolysis.108,201,203 Besides these products, a wide variety of products have been detected and quantified in the literature for the ozonolysis of Limonene. This

148 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

includes the formation of carbonyl compounds, hydroperoxides and even secondary ozonide. 201,204,205

Ozonolysis of limonene proceeds by the dipolar addition of ozone into either the endo- or the exo-double bond. It is believed that the addition rate of O3 to the endo-double bond proceeds at a factor of 10-50 faster than the addition to the exo- 206 double bond under low NOx (i.e., low NO + NO2). For discussion purposes, only the addition to the endo-double bond is considered. The concerted addition to the double bond is highly exothermic, releasing about 47-64 kcal mol-1 of energy and the resulting compounding with a five-membered ring is called a primary ozonide (POZ, Scheme 5.1).207 This excess energy is retained in the molecule resulting in the prompt decomposition of the POZ. Homolytic cleavage of the C-C bonds and one of the O-O bonds yields two different isomeric products, CI1 and CI2, with a carbonyl and a carbonyl oxide (Criegee intermediate, CI) functionality tethered to the molecule. These products can undergo a 1,3-dipolar cycloaddition to yield secondary ozonides (SOZ), although this is unlikely in the gas phase unless a high concentration of ozone is used or compounds to trap the Criegee intermediates are used.208,209 For linear alkenes, the carbonyl and the CI are detached following the decomposition of the POZ. These channels of decomposition of the CI can be via the ester channel, O-atom elimination or the hydroperoxide channel. 1 The ester and the hydroperoxide channels are important as one of the products from these pathways is the hydroxyl, OH radical which is the primary oxidant in the atmosphere. 210,211 Therefore ozonolysis reactions can be an important source of OH radicals during evening and night when other production channels for OH are not active. 212

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 149

Scheme 5.1: Scheme depicting the ozonolysis of limonene and the production of Criegee intermediate products (CI1 and CI2) and secondary ozonide. The Criegee intermediate products can undergo rearrangement reactions to yield the suggested m/z 183 products.

150 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

5.3.2 Monitoring changes to the mass spectrum profile

The changing profile of the negative ion mass spectrum was observed when different variables in the experiment were changed as indicated in the total ion chromatogram (TIC) trace shown in Figure 5.7. The mass spectra shown below represent the integrated mass spectra for each stage of the experiment which are colour coded. The negative mode mass spectrum (m/z 50 – 1000) was continuously acquired through the different experimental stages. The change in ozone concentration as well as the particle counts as measured by the particle counter were plotted along with the TIC trace for the duration of the run in Figures 5.8 (a) and (b), respectively.

Figure 5.7: The (-) ion TIC trace for the limonene ozonolysis experiment in given in panel (a). Panels b – f shows the integrated mass spectrum across the TIC for the duration of each experimental stage which is colour coded. Panel (g) shows the O2 blank spectrum prior to the introduction of ozone in the reaction chamber.

The experiment involved five different steps; ‘Limonene pre-injection’,

‘injection with no filter’, ‘filter’, ‘no filter’ and ‘O3 off’. These stages were a part of an hour long data acquisition. The area under the TIC curve that was measured prior to injection into the reaction chamber is labelled in pink in Figure 5.7(a). This shows

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 151

the overall low number of ions generated by the ESI in the absence of limonene vapour. The mass spectrum acquired by integrating the ion abundance across this region is shown in Figure 5.7(b) and represents only background ions generated largely by low level contaminants in the ESI solvent. For example, the ions at m/z 255 and m/z 281 correspond to the fatty acids commonly reported in the negative ion ESI of methanolic samples.213 Figure 5.7(c) shows the integrated mass spectrum for the blue region in the TIC. Particles were formed when limonene was injected at the start of this stage of the experiment. The mass spectra shows the characteristic profile of an aerosol mass spectrum and is strictly similar to the mass spectra obtained by Laskin and co-workers for their off-line analysis of limonene SOA.108 The next stage in the experiment involved switching the aerosol flow through a filter and the ions produced by ESI as given in the TIC is coloured yellow. When the aerosol is made to pass through the filter, there is a steady decrease in the total number of ions generated as indicated by the TIC. This suggests that perhaps some of these particles are being trapped by the filter resulting in diminishing ion counts. It should also be noted that in these experiments, a denuder was not used. Therefore, gas phase products formed can freely pass through the filter if they are not consumed by heterogeneous chemistry occurring on the particle surface. The integrated mass spectrum for this part of the experiment is given in Figure 5.7(d). The aerosol mass spectrum profile changed compared to the spectrum in Figure 5.7(c). Notably, there was a reduction in the ion abundances for the group of ions in the mass range of m/z 300 – 450. Compounds with high molecular weights (m/z 300) have been found to constitute a major fraction of SOA components.111 This suggests that these compounds which were formed in the reaction chamber during ozonolysis are being trapped by the filter paper. These quartz filters have particle retention of 99.95 % for 0.3 µm particles and are routinely used for atmospheric particulate sampling. Lab generated particles formed from monoterpene ozonolysis can reach up to 300 nm in size under ‘dry’ conditions.202 Although humidity was not measured in the experiments reported here, there is an indication that some of these particles from the mass range of m/z 300 – 450 are indeed being trapped by the filter.

Further evidence of this comes from the integrated spectrum obtained for the next stage of the experiment as given in Figure 5.7(e) and indicated by the colour orange in the TIC. In this stage, the aerosol particles were diverted directly to the ESI

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source rather than passing through the filter. Interestingly, the spectrum obtained looks very similar to the one obtained in Figure 5.7(c). This provides further evidence for entrapment of particles by the filter. For the final stage, the ozone was switched off and the ions generated in this stage as shown in the TIC are indicated in green. The resulting integrated mass spectrum for this region in Figure 5.7(f) shows a reduction of ions in the higher mass range between m/z 300 – 450. This could indicate the cessation of reactions responsible for the generation of ions in this mass range as the ozone as shut off. Figure 5.7(g) shows the O2 blank spectrum prior to the introduction of ozone in the reaction chamber. This spectrum is indicative of background ions generated, mostly by low level contaminants.

5.3.3 Variability in ozone concentration and ion counts

The relative abundances of the ions are changing as the experiment proceeds in the second stage of the experiment as given in Figure 5.7(a). This variability in the TIC relative abundances seems to correlate with the changes in ozone concentration which was supplied to the reaction chamber as evident in Figure 5.8(a). It is well understood that product distributions vary with the ozone concentration and this is evident during the experiment. This indicates that the on-line analysis is very sensitive to changing product distributions because of changing ozone concentrations. During Stage 3, when sampling of the aerosol particles through the filter took place, the TIC relative abundances were slowly decreasing and for the next stage, when the filter was by-passed, the ion counts promptly increased as expected. When ozone generation was shut down in the last stage, the ions produced dropped as well. This could be due to the reduced number of particles forming in the absence of ozone or products that were still forming were not ionisable using EESI.

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Figure 5.8: The variation of ozone concentration (a) and the particle concentration (b) overlayed on top of the total ion chromatograph trace for the limonene ozonolysis experiment.

5.3.4 Particle number concentration

The particle number concentrations were measured using a condensation particle counter. Upon injection of the limonene, the CPC data shows that the particle number concentration reached the maximum particle count of 1 x 107 particles cm-3 upon the injection of limonene (Figure 5.8(b)). This dramatic rise in the particle number concentration represents the realisation of the high aerosol formation potential of limonene during ozonolysis.135 This value was the maximum number of particles the instrument could analyse. The particle counts could have been reduced by dilution of the aerosol after its generation prior to entering the CPC for analysis but that was not carried out in the experiment. During ozonolysis, new particles can form from homogeneous nucleation of the ozonolysis products with very low volatilities. Furthermore, the ozonolysis products can also condense on pre-existing

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particles. However, the number of new particles that is formed is very small and can be regarded as a minor source of particles in this experiment. However, it is impossible to differentiate the chemical composition of new particles and compositions of particles with condensed ozonolysis products. When the O3 production was shut down in stage 4, the particle counts dropped to 0 within a few minutes.

5.3.5 Off-line filter paper analysis

The filter papers were subjected to off-line analysis using ESI in the negative mode. A filter paper was sampled while having ozone pass though it for 10 mins in the absence of limonene and limonene ozonolysis particles at the start of the experiment and was subject to the same extraction procedure as the filter sampled during the experiment. The extract from this filter is termed ‘Filter blank extract’. Figures 5.9 (a) and (b) shows the negative mode ESI mass spectrum of the blank and sampled filter extracts respectively. The abundant m/z 255 and 288 peaks are present in the blank sample and could be because of impurities in the filter and/or the solvent spray. The mass spectrum of the filter extract shows a collection of peaks in the 150 – 200 m/z mass region. Peaks at m/z 169, 177, 183, 185, 199 and 201 are indicative of ions from the sampled aerosol during the third stage of the experiment when the aerosol particles were sampled through a filter, as they are absent in the blank filter extract. Ions with m/z 169, 183, 185, 199 and 201 were also detected in an off-line analysis using ESI-TOF MS analysis. 197 Ions with larger masses in the region of m/z 300 – 450 was expected in the aerosol sample filter because ions with these masses were reduced in the TIC when the aerosol flow was directed through the filter. However, these smaller masses could have been the building blocks of those larger masses and were fragmented during the extraction process. These ions are thought to be from particle phase carboxylic acid products produced during ozonolysis reactions. Even though the aerosol was sampled through the filter for 10 mins, the entrapment of some of the particle phase products was successful.

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Figure 5.9: A filter was sampled for 10 mins with ozone passing through in the absence of limonene ozonolysis particles at the start of the experiments and another filter paper was sampled with the limonene ozonolysis particles during the second stage of the limonene ozonolysis experiments. The resulting (-) ESI mass spectrums of the extracts of these filters are given. Panel (a) is the mass spectrum for the filter blank extract and panel (b) is the mass spectrum for the filter aerosol extract.

5.3.6 Online analysis of 1-cyclohexene carboxylic acid ozonolysis

A similar experiment to the one outlined above for limonene ozonolysis was carried out in another day for 1-cyclohexene carboxylic acid (1-CCA). Figure 5.10(a) shows the TIC obtained from the limonene ozonolysis experiment. Prior to the injection of 1-CCA as indicated by the region in pink, the ion counts are low at about 10%. Upon injection, the ion counts jump and are fluctuating throughout this stage of the experiment as shown by the area in blue. When the aerosol flow is directed through the filter as indicated by the region in yellow, the ion counts fall to pre- injection levels of about 10%. Diversion of the aerosol flow such that the aerosol flow by-passes the filter, resulted in an increase in the ion counts.

156 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

The mass spectrum obtained for each experimental stage was integrated across the stages which are colour coded.

Figure 5.10: Panel (a) shows the (-) ion TIC for the 1-CCA ozonolysis experiment. Panels b – e shows the integrated EESI mass spectrum for the colour coded regions in the TIC. Panel (f) shows the EESI blank mass spectrum obtained while having only O2 in the reaction chamber.

Figure 5.10 (b) shows the EESI integrated mass spectrum for the region in the TIC prior to the injection of 1-CCA. The spectrum is representative of back ground ions composed of low levels of contaminants. Panel (c) shows the mass spectrum for second stage of the experiment when 1-CCA in methanol was injected into the reaction chamber in the presence of ozone. The abundant m/z 125 ion corresponding to the anion of 1-CCA ([M-H]-) appeared instantaneously upon injection in the reaction chamber. This was not possible with the limonene as it is not readily ionised in the negative mode. The other ions which were present in the mass spectra were present at less than 10% abundance. A major difference between the limonene experiment and this was that after injection, there was no aerosol plume observed when 1-CCA was injected. Also, the mass spectrum did not exhibit the characteristic

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groups of peaks indicative of aerosol formation. Panel (d) shows the integrated mass spectrum when the gas flow was directed through the filter. Although the m/z 125 ion is still present, there are many other ions present, which are mostly solvent contaminant peaks. The reason for this could be that when the gas flow was directed through the filter, the ions counts were reduced as indicated by the TIC for this stage and as a result, there were fewer ions available for extraction through EESI. Therefore, most of these newer peaks could be from the contaminants in the methanol spray solvent. When the filter was by-passed in the next stage, the mass spectrum as shown in panel (e) was similar to the mass spectrum shown in panel (c). This was also seen during the limonene ozonolysis experiment; when the gas flow was reverted, by-passing the filter, the mass spectrum profile looked identical to the one obtained prior to directing the gas flow through the filter. Panel (f) shows the integrated EESI spectrum obtained prior to the experiments while having only O2 in the reaction chamber.

5.3.7 Particle concentration and variability in ozone concentrations

Figure 5.11 shows the changes in ozone concentration and particle counts superimposed on the TIC counts from the 1-CCA ozonolysis experiment. Figure 5.11 (a) shows that the concentration of ozone in the reaction chamber was fluctuating throughout the experiment similar to what was obsereved during limonene ozonolysis. However, unlike the limonene experiment, the change in TIC does not show any correlation to the ozone concentration. Figure 5.11 (b) shows the change in the particle counts as measured by the CPC. There was no drastic change in the particle concentration when the 1-CCA was injected at the 3 min mark. Although there was a temporary spike in the particle counts, later on, the particle counts was not maintained. This is consistent with the observation during the experiment that there was no aerosol cloud observed when the 1-CCA was injected. This implies that aerosol formation did not occur when 1-CCA was injected and hence, no secondary chemistry occurred. This could be because the 1-CCA was diluted while the limonene experiment utilised the neat undiluted compound. Also, since it was dissolved in methanol, the compound could have been retained in the solution phase rather than being abundant in the vapour phase, due its polar interactions with the solvent and was effectively shielded from the interaction with ozone.

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Figure 5.11: The variation of ozone concentration (a) and the particle concentration (b) overlayed on top of the total ion chromatograph trace for the 1-CCA ozonolysis experiment.

5.4 Conclusion

An online mass spectrometry analysis suited for the analysis of aerosols generated from limonene ozonolysis was developed by modifying a pre-existing electrospray ionisation interface. The analysis using EESI was applied for the first time to the real-time analysis of the ozonolysis of limonene. The experiment provided high time resolution and the limonene aerosol spectrum obtained showed striking resemblance to the spectrum using an off-line method. 108 The results also highlight that the rather simple on-line extraction procedure can be applied to other

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biogenic terpenes. This simple modification adds to the existing body of knowledge for the development of new methods to study secondary organic aerosol formation in real time. The experimental set-up described here is rather simple compared to other groups; the experiment could be improved in the future by adding a denuder as well as including a way to dilute the aerosol particles formed prior to its measurement in the CPC. While the charge-tagging approach failed to produce any aerosols in the reaction chamber, future work can be conducted by utilising higher concentrations of the compound or by using compounds with higher vapour pressure and other functional groups.

160 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

Chapter 6: Summary and Conclusions

In this dissertation, gas phase studies of the ozonolysis of 1- and 3- cyclohexene carboxylates and iodide ions were utilised to understand the reaction kinetics and product distributions from ion-molecule reactions of these compounds. To facilitate these investigations, a linear quadrupole ion-trap was modified to enable the introduction of O3/O2 mixture of gas into the buffer gas of the mass spectrometer. Also, an experimental set-up to accommodate the real-time analysis of laboratory generated aerosols was demonstrated. D-Limonene was utilised as the precursor of the aerosols and extractive electrospray ionisation (EESI) was used as an ionisation technique.

6.1 Gas phase reactions of cyclohexene carboxylate anions with ozone

Reactions of endo-cyclic alkenes with ozone are thought to occur in the atmosphere. To study such reactions using a linear ion-trap mass spectrometer, a charge tagged approach was employed. 1- and 3-cyclohexene carboxylate anions were generated using negative mode ESI. Isolation of 1-cyclohexene carboxylate anion in the presence of ozone resulted in the formation of a carbonate radical anion as a major product. This m/z 60 product was previously found to form from the reaction of α-carboxylate radical anion with dioxygen. 144 The resulting peroxyl radical product interacts with the carboxylate moiety resulting in the formation of a •- - carbonate distonic ion (CO3 ). Ozonolysis of the [1-CCA-H] ion results in the formation of primary ozonide and the subsequent O-O bond homolysis can result in the formation of the α-carboxylate peroxyl radical anion (Scheme 6.1). This then forms the m/z 60 ion through interaction with the carboxylate head group.

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Scheme 6.1: The production of m/z 60 ion from the ozonolysis of 1-cyclohexene carboxylate ion.

The production of the m/z 60 ion deviates from the products predicted by the Criegee mechanism of ozonolysis.117 The Criegee mechanism predicts the formation of a Criegee intermediate diradical and a carbonyl compound tethered to the molecule.

Besides the rupture of the O-O bond, the homolysis of the C-C bond in the cyclohexene moiety is also necessary to form the diradical intermediates but in Scheme 6.1, the C-C bond is presumed to be intact.

The m/z 60 product was formed in a very minor abundance for the ozonolysis of the other isomer, 3-cyclohexene carboxylate anion. Ozonolysis rates for the [1- CCA-H]- ions was determined to be 12.5 times faster than the ozonolysis rate for the [3-CCA-H]- isomer. The reaction efficiencies were 8.5% and 0.7%, respectively. This enhanced ozonolysis rate for the [1-CCA-H]- isomer is rationalised as arising from substitution of the carbon-carbon double bond in this isomer. Not only is the double bond in [1-CCA-H]- ion more substituted, conjugation effects into the carboxylate moiety enhanced the nucleophilic character of the double bond. Also, the presence of an electron donating group next to the double bond also enhances the reaction rate. Isolation of the other isomer, 3-cyclohexene carboxylate in the presence of ozone did not yield any major products.

162 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

Computational predictions revealed that the ozonolysis of 1- and 3- cyclohexene carboxylate anions is exothermic by about -60 kcal mol-1, which is similar to energies for the ozonolysis of their neutral counterparts. Furthermore, computational study revealed that the m/z 141 product could also be a β-lactone product. This product is thought to be formed from a charged induced decomposition of the primary ozonide.

Although the charge tagging approach was clinical to the study of these compounds using mass spectrometry, charge loss processes dominated the reactions. This resulted in the loss of ion signal. Ionised products, which would have been expected from solution phase ozonolysis, were not observed in the gas phase.

6.2 Gas phase reactions of iodide and bromide anions with ozone

Fundamental gaps in our understanding of the ozonolysis of halide ions exist in the literature even though the evidence of these processes occurring on air-snow interfaces is increasing. To study the reaction kinetics as well as product distribution of such reactions, the study of the gas phase ozonolysis reaction of I- was undertaken. Experiments revealed a remarkable previously over-looked stepwise mechanism for - the formation of IO3 in the gas phase. In the presence of excess ozone, therefore - - under pseudo-first order conditions, I ions react with ozone forming iodate ions, IO3 - - . Also, present in the mass spectrum were products IO and IO2 in low abundance. In order to facilitate the generation of these ions in high abundance, an in-source ozonolysis technique was applied which utilized oxygen as a nebulising gas and used 101 - - high capillary voltages. The resulting abundant IO and IO2 ions were individually mass selected and isolated in the presence of ozone and their reaction kinetics determined. The reaction between IO- and ozone was found not to follow pseudo-first order kinetics and that the reaction was reversible. Trapping the - - ozonolysis product, IO2 in the presence of oxygen resulted in the formation of IO - ion. However, the forward reaction was a faster reaction. The reaction between IO2 and ozone adhered to pseudo first-order kinetics and the reaction was reversible as well. The forward reaction was found to be very fast and that the formation of the - IO2 ion was the rate limiting step in the overall reaction scheme.

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Scheme 6.2: The sequential oxidation steps of the iodide ion with ozone.

The reaction between the Br- ion and ozone was intrinsically slow compared to I- ion ozonolysis. However, in the ozonolysis mass spectrum obtained, BrO- and - BrO.H2O ions were observed. Therefore, these products imply that the same step- wise oxidation process could occur for the ozonolysis of Br- ion.

High level computational studies at the UCCSD/6-311+G(d,p) level of theory - - suggests that at least on the singlet surface, the reaction of BrO and O3 and BrO2 -1 nd rd and O3 are exothermic by 30.2 and 140.4 kJ mol . The barrier for the 2 and 3 O- addition steps are lower than the first.

6.3 Development of a charge-tagging approach for the characterisation of chemical intermediates in the formation of secondary aerosols from the ozonolysis of cyclohexenes

Experiments undertaken in Chapters 3 and 4 was concerned with the production and isolation of an ion in the ion-trap for the observation of ion-molecule reactions. However, the elucidation of particle phase products is also important in understanding, multi-phase, heterogeneous chemistry occurring at the aerosol interface. To enable this online investigation of gas and particulate products of ozonolysis, an aerosol generation and subsequent on-line analysis experimental set- up was described. The experiment involved the production of aerosols from d- Limonene and the subsequent aerosol generated was analysed using extractive electrospray (EESI). D-Limonene was chosen as it exhibits a high aerosol forming

164 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

potential.116 However, unlike the [1-CCA-H]- ion for example, it is not readily ionisable in the negative ion mode. Regardless, the products of limonene ozonolysis have been fairly well elucidated using a suite of off-line methods.

The on-line EESI mass spectrum obtained showed a striking resemblance to the off-line mass spectrum obtained in the literature.108 Aerosol production was confirmed visually and experimentally using a particle condensation counter. Using an automated data dependent routine during the acquisition of data, it was possible to obtain some aspects of chemical information in real-time via the collision induced dissociation mass spectra of the most abundant ions. These ions were characteristic of carboxylic acids. However, this meant that the resulting data set was large.

D-Limonene is a neutral compound and is not detected in our experiments. It was not possible to monitor its consumption directly using the experimental set-up employed. Thus, it was postulated that a charge tagged approach might make this feasible. However, injection of the 1-cyclohexene carboxylic acid dissolved in methanol into the reaction chamber containing ozone did not result in the formation of aerosol particles. This was confirmed again, visually as well as from the CPC data. It could be that the compound was locked in the condensed phase due to the polar interactions with methanol and was not exposed intact with ozone in the reaction chamber.

Overall, these experiments show the utility and the versatility of mass spectrometry in probing reaction kinetics and product distribution in ion-molecule studies. While further improvements for the on-line analysis of aerosols in the field are expected, the experiments undertaken showed that mass spectrometry coupled with the EESI ionisation technique is ideal for the real-time analysis of aerosols generated from the ozonolysis of biogenic terpenes. The information gathered from the real-time screening of aerosol will imply the generation of large datasets which needs to be analysed using data tools.

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6.4 Future work

The gas phase reactions of cyclohexene carboxylate anion with ozone could be investigated in the future by using compounds where there is some degree of charge separation in its structure. By distancing the charged moiety further from the location of the double bond, the effects of the charge on ozonolysis rates and product distributions can be studied.

The temperature dependence of the ozonolysis reactions explored in this thesis could be investigated. The kinetic data obtained were obtained at 307 K which is an atmospherically relevant temperature and further experiments conducted at higher and lower temperature will be useful.

While the relative pseudo-first order kinetics of the gas phase reactions of iodide anions, hypo-iodide and iodite with ozone were determined, true 2nd order rate constants are yet to be determined. The 2nd order rate constant could be determined by determining the exact concentration of ozone in the ion-trap and measuring the relative concentrations of the precursor and product ions at different concentrations of ozone. One way to determine the ozone concentration is by using a spectrometric method. A spectrometer could be installed into the ozone-mixing manifold. The

O2/O3/He mixture could then be directed to a flow cell where a UV measurement can take place and hence the ozone concentration determined using the Beer-Lambert law.

Experiments conducted for the characterisation of chemical intermediates in the formation of secondary aerosols from the ozonolysis of cyclohexenes can be further refined. For instance, the failure to observe any aerosol formation from 1- CCA was postulated to be because of the use of methanol as a solvent. In future experiments, the vapour of 1-CCA can be introduced directly into the reaction chamber. This could minimise any solvent effects which can supress secondary particle formation. Furthermore, the aerosol plume once formed could be diluted so that meaningful measurements by the condensation particle counter could be made. This could provide meaningful particle size information which could be used to determine the subsequent growth of the aerosol particle for instance.

In summary, state-of-the-art experimental techniques and instrumentation described in this dissertation were used to characterise one of the most important

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atmospheric chemical reactions – the ozonolysis reactions in the gas and particle phase, respectively and new secondary aerosol formation and growth. This thesis contributes to the knowledge about the gas phase reactions of cyclohexene carboxylate anions and iodide and bromide anions with ozone, as well as characterization of chemical intermediates in the formation of secondary aerosols from the ozonolysis of d-Limonene.

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182 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

Appendix A

A.1 Computational methods

Theoretical computations were performed on the QUT’s HPC cluster and also on the National Computational Infrastructure (NCI) Raijin cluster using the Gaussian 09 software package.136 Geometry optimisations of all reactants and products were executed using hybrid density functional theory (DFT). Optimisation and bench- marking of appropriate functionals was undertaken (see below) and the selected methods were Becke’s three-parameter hybrid employing the LYP correction function (B3LYP) in conjunction with the split valence diffuse, polarized basis set 6- 31+G(d,p) for cyclohexene ozonolysis calculations. Stationary points were characterized as either minima (no imaginary frequencies) or transition structures (one imaginary frequency) by calculation of the frequencies using analytical gradient procedures. The minima connected by a given transition structure were confirmed by intrinsic reaction coordinate (IRC) calculations. Zero-point energy corrections for the electronic energies have not been included.

A.2 Benchmarking of computational method

Computational investigations of ozonolysis reactions on rather small model systems have previously been conducted using a wide range of theoretical methods.125,214 In the present investigation it will be necessary to calculate the reaction energetics of both intermediate small sized alkenes (e.g., ethene) and larger alkenes (e.g., deprotonated 1-and3-cyclohexene carboxylic acids). Therefore a range of computationally efficient DFT methods were benchmarked against a high-level ab initio study for the model reaction of propene and ozone.139

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 183

1. Geometry

The structures of propene, ozone and the corresponding trioxolane from the ozonolysis reaction were optimised using four different levels of theory and nine different basis set (including eight Pople-type and one Dunning-type basis sets). B3LYP hybrid density functional theory, CAM-B3LYP, ω97XD and M06-2X were used for geometry optimization and vibrational frequency calculations.215–218 Stationary points were characterized as a minimum on the basis of all the calculated vibrational frequencies being real.

The experimental values for the carbon-carbon single and the double bonds in propene are 1.501 and 1.336 Å respectively.219 The computed carbon-carbon (C-C) and carbon-carbon double bond (C=C) bond distances for propene were similar for the different levels of theory with the different basis sets. The data are summarised in Table A.1 and show that they differ from each other and the experimental benchmark by less than 0.02 Å. The mean absolute deviation for the calculated values for the C-C single bond and the C=C double bonds for the B3LYP level of theory is 0.00086 and 0.003 Å, respectively (this excludes the value for calculated bond lengths using the aug-cc-pVTZ basis set).

Theory/Basis Set r1 r2 (A) (A) B3LYP/6-311G(d,p) 1.501 1.329 B3LYP/6-31+G(d) 1.503 1.337 B3LYP/6-311+G(d,p) 1.500 1.331

184 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

B3LYP/6-31G(d) 1.502 1.333 B3LYP/6-31+G(d,p) 1.503 1.337 B3LYP/6-31++G(d) 1.503 1.337 B3LYP/6-31++G(d,p) 1.502 1.337 B3LYP/aug-cc-pVTZ 1.497 1.327 M062X/6-31+G(d) 1.501 1.332 M062X/6-31++G(d) 1.501 1.332 M062X/6-31++G(d,p) 1.500 1.332 M062X/aug-cc-pVTZ 1.496 1.324 WB97XD/6-31+G(d) 1.501 1.333 WB97XD/6-31++G(d) 1.501 1.333 WB97XD/6-31++G(d,p) 1.500 1.333 WB97XD/aug-cc-pVTZ 1.495 1.324 CAMB3LYP/6-31+G(d) 1.499 1.331 CAMB3LYP/6-31++G(d) 1.499 1.331 CAMB3LYP/6-31++G(d,p) 1.499 1.331 CAMB3LYP/aug-cc-pVTZ 1.493 1.321 Experimental 1.501 1.336 Table A.1: The C-C and C=C bond lengths in the gas phase propene structure as calculated from the different levels of theory and basis sets indicated. The experimental values from literature are also presented for comparison.219 The calculated values are the calculated equilibrium geometric parameters and the experimental value from literature experimental ground state, vibrationally averaged geometric parameters.

For ozone, the experimental values for the O-O bond length and the O-O-O bond angle are 1.272 Å and 116.8°, respectively.220 The B3LYP theory approximated closely the experimental values for a range of different basis set (Table A.2). B3LYP/6-31G(d), B3LYP/6-31+G(d,p), B3LYP/6-31++G(d), B3LYP/6-31++G(d,p) all gave O-O distances of 1.264 Å, the O-O-O bond angles were 117.9, 118.1, 118.1 and 118.1°, respectively (see Table 2). The O-O distances were all underestimated (by about 0.03 Å) when the other 3 theories were used. The mean absolute deviation for the O-O bond length is 0.0035 Å and for the O-O-O bond angle is 0.09° for the B3LYP level of theory utilizing the different basis sets. Although the ω97XD and

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 185

CAM-B3LYP levels of theory predicted the closest values to the experimental (O-O- O) bond angle values, O-O bond length were off by about 0.014 Å. However, the difference between the predicted bond lengths using the B3LYP level of theory and experiment was only about 0.008Å.

r1 (Å) O-O-O Theory/Basis Set angle a1 (°) B3LYP/6-311G(d,p) 1.258 118.2 B3LYP/6-31+G(d) 1.263 118.1 B3LYP/6-311+G(d,p) 1.256 118.4 B3LYP/6-31G(d) 1.264 117.9 B3LYP/6-31+G(d,p) 1.264 118.1 B3LYP/6-31++G(d) 1.264 118.1 B3LYP/6-31++G(d,p) 1.264 118.1 B3LYP/aug-cc-pVTZ 1.255 118.3 M062X/6-31+G(d) 1.239 118.2 M062X/6-31++G(d) 1.239 118.1 M062X/6-31++G(d,p) 1.239 118.1 M062X/aug-cc-pVTZ 1.232 118.1 WB97XD/6-31+G(d) 1.248 117.9 WB97XD/6-31++G(d) 1.248 117.9 WB97XD/6-31++G(d,p) 1.248 117.9 WB97XD/aug-cc-pVTZ 1.239 118.1

186 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

CAMB3LYP/6-31+G(d) 1.249 117.9 CAMB3LYP/6-31++G(d) 1.249 117.9 CAMB3LYP/6-31++G(d,p) 1.249 117.9 CAMB3LYP/aug-cc-pVTZ 1.241 118 Experimental 1.272 116.8 Table A.2: The O-O bond lengths and bond angles of gas phase ozone as calculated from the levels of theory and basis sets as indicated. The experimental values obtained from the literature are also presented.220 The calculated values are the calculated equilibrium geometric parameters and the experimental value from literature experimental ground state vibrationally averaged geometric parameters.

In general, no combination of a theory and a basis set predicted the exact values for the C-C and C=C bond lengths for propene when compared to the experimental values. Furthermore, this was the case for the O-O bond lengths and O- O-O bond angles for ozone.

Besides the aug-cc-pVTZ basis set, combinations of the different theories and basis sets gave good approximation of the C-C bond lengths. The M062X and ω97XD level of theory gave the exact values for the C-C bonds when paired with the 6-31+G(d) and 6-31++G(d) basis sets. However, these levels of theory and basis sets were not as accurate in predicting the C=C bond lengths for propene as the B3LYP level of theory and the 6-31+G(d), 6-31+G(d,p), 6-31++G(d) and 6-31++G(d,p). The B3LYP level of theory coupled with basis sets with diffuse and polarised functions gave the most accurate geometries when both the ozone and propene geometries are concerned.

2. Energies

Table A.3 summarises the available literature for calculation of the reaction energies for the process described in Scheme A.1 for a range of different alkene- ozone systems using different theoretical approaches. These results suggest that reaction energies for the initial adduction of ozone onto and alkene are in the range of 48-62 kcal mol-1 indicating these to be highly exothermic processes. The high level computational study of Vayner et al. on the reaction of propene with ozone was

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 187

selected as a benchmark calculation.139 Initially, to replicate the benchmark, a single point calculation using CCSD(T)/aug-cc-pVTZ//B3LYP/6-31+G(d,p) was carried out for propene, ozone and the 1,2,3-trixolane structures. The calculated reaction energy (cf. Scheme A.1) was 60 kcal mol-1.

Scheme A.1: The addition of ozone to propene; the process is exothermic by 60 kcal mol-1. The value is obtained from a single point calculation using CCSD(T)/aug-cc- pVTZ//B3LYP/6-31+G(d,p).

Ozonolysis Species Method Energies (kcal mol-1) Propene139 CCSD(T)/cc-pVTZ // B3LYP/6-31G(d) 62(syn), 61.1(anti) 1,3-butadiene (E,Z)129 CCSD(T)/6-311G(d,p) // B3LYP/6-311G(d,p) 50(cis), 48(trans) Cyclohexene154 B3LYP/6-31G(d) 61.8 Ethylene127 CCSD(T)/6-311G(2d,2p) // B3LYP/6-31G(d) 55.2 1,1-difluoro ethylene221 QCSID(T)/cc-pVDZ // MPW1/cc-pVTZ 59.9 Table A.3: The exothermicity of the primary ozone relative to the reactants in selected literature. The “//” represents combination of an optimisation method followed by a higher level single point calculation of the energies.

Calculations by Vayner et al., showed that the molozonide formation releases about 60 kcal mol-1 of energy (60.2 kcal mol-1 for the syn-primary ozonide and 59.5 kcal mol-1 for the anti-primary ozonide).139 Subsequently, using the CCSD(T) ab initio method, they obtained an energy value of 62 kcal mol-1 for the syn-primary ozonide formation and 61.1 kcal mol-1 for the anti-primary ozonide formation. Their results could be reproduced in this benchmarking.

188 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

The DFT methods along with a wide suite of basis sets were used to evaluate the reaction energy of ozone addition to propene with the results are summarised in Figure A.1. For the hybrid-DFT B3LYP the maximum reaction energy (70 kcal mol- 1) is obtained using the 6-311G(d,p) while the lowest (57 kcal mol-1) is found using the aug-cc-pVTZ basis set. Adding polarization and diffuse functions to the split valence basis sets (6-31G) has little impact on the overall energy but using a triple split valence basis set (6-311G) does affect the energies considerably for instance the 6-311G(d,p) and 6-311+G(d,p) significantly over-estimated the reaction energies. The average energy using 9 different basis set is 62 kcal mol-1.

B3LYP M062X WB97XD CAM-B3LYP -40

-45 6-31G(d) -50 6-311G(d,p) 6-31+G(d) -55 6-31+G(d,p) -60 6-31++G(d) 6-31++G(d,p) -65

Energies in kcal/mol 6-311+G(d,p) -70 6-311++G(d,p) aug-cc-pVTZ -75

-80 Levels of theory

Figure A.1: The reaction energy for ozone addition to propene as calculated using four different levels of theories and 9 different basis sets. The energies are not zero- point corrected. The black line corresponds to the energy of -62 kcal mol-1 is the recommended value based on Vayner et al. for the addition of ozone to propene obtained from a single point CCSD calculation after the primary ozonide’s geometry was optimised at the B3LYP/6-311G(d,p) level of theory.139

Zhao and Truhlar recently developed the M06 family of local (M06-L) and hybrid (M06, M06-2X) functional, which show promising performance for noncovalent interactions that may be important in describing pre-reactive complexes in the gas phase chemistry of ozone and alkenes.218 The M06-2X functional was

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 189

recommended for calculations for main group thermochemistry, kinetics and thermochemistry and thus this functional was employed in this study. Interestingly, the M06-2X hybrid functional overestimates the reaction energy by about 15-20 kcal mol-1 (see Figure A.1). The highest energy obtained for the trioxolane formation was 81 kcal mol-1 using the 6-31+G(d) basis set and the lowest was 74 kcal mol-1 for the aug-cc-pVTZ basis set. The average energy using these basis sets was 77 kcal mol-1; about 17 kcal mol-1 higher than the literature benchmark.

Prior to the addition of ozone to the alkene a van der Waals complex may be important in dictating reaction kinetics.156 Dispersion interactions such as the van der Waals-type interactions are thus potentially important for large systems where inclusion of these interactions in theoretical simulations are important for an accurate representation of chemistry. The ωB97-XD functional accounts for this dispersion interaction and has been shown to yield satisfactory accuracy for the thermochemistry, kinetics and non-covalent interactions.217 The benchmarking data shown in Figure 3 suggest that the ωB97-XD functional overestimates the energy released in the initial trioxolane formation but not to the same extent as M06-2X. For the ωB97-XD functional, the highest reaction energy was found with the 6-31G(d) basis set at 67.65 kcal mol-1 and the lowest with the aug-cc-pVTZ basis set at 63.70 kcal mol-1. The average of calculated energies was about 67 kcal mol-1, which is significantly greater than the benchmark value. Very modest changes in the calculated energies were observed for the split valence shell basis sets with varying diffuse and polarization functions. Out of the four levels of theories compared, the ωB97-XD had the least amount of deviation between the basis sets.

The CAM-B3LYP functional is an extension to the B3LYP functional. This functional splits the exchange interaction operator into long and short range components. It has been shown that this method yields similar ionisation potentials and bond lengths and shows improvement on the classical reaction barriers compared to the B3LYP functional.6 Despite these reported improvements, the CAM-B3LYP level of theory also overestimated the reaction energy by as much as 12 kcal mol-1. The highest energy corresponded to the 6-31G(d) basis set at 72.73 kcal mol-1 and the lowest was obtained using 6-311++G(d,p) 64.64 kcal mol-1. The average

190 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

calculated energy was about 68 kcal mol-1 significantly above the benchmark and the value obtained from the unmodified B3LYP functional (see above).

3. Energies for propenoate ion ozonolysis using high level CCSD(T) single point calculations.

Single point high level CCSD(T) calculation were obtained for the primary ozonide from the reaction between propenoate ion and ozone. Initially, the geometry was optimised using three different theories (B3LYP, M06-2X and ωB97-xD) and two different basis sets (6-31+G(d,p) and aug-cc-pVDZ). Subsequently, single point calculations at the CCSD(T)/cc-pVDZ level of theory were carried out on the optimised geometries. The values are given in Table A.4.

Theory/Basis set Energy (kcal mol-1) Single point energy (kcal mol-1) B3LYP/6-31+G(d,p) -59.8 -62.6 B3LYP/aug-cc-pVDZ -77.8 -62.5 M06-2X/6-31+G(d,p) -78.0 -63.1 M06-2X/aug-cc-pVDZ -76.0 -63.9 ωB97-xD/aug-cc- -65.1 -63.1 pVDZ

Table A.4: Single point CCSD(T)/cc-pVDZ energies for primary ozonide formation from the reaction between propenoate ion and ozone calculated from geometries optimised from either the B3LYP, M06-2X or ωB97-xD theories combined with either the 6-31+G(d,p) or aug-cc-pVDZ basis sets.

Table A.4 shows contrasting energies for the optimised geometries for the primary ozonide from the reaction between propenoate ion and ozone. For instance, at the B3LYP/6-31+G(d,p) level of theory, the energy is -59.8 kcal mol- 1 but when employing the dunning basis set, aug-cc-pVDZ at the same level of theory, the energy value is -77.8 kcal mol-1. However, the energy values are similar when using these two basis sets at the M06-2X level of theory. Using the 6-31+G(d,p) basis set gave an energy of -78 kcal mol-1 and using the aug-cc- pVDZ resulted in the value of -76 kcal mol-1. Attempts at obtaining an optimized structure for the primary ozonide at the ωB97-xD/6-31+G(d,p) was not successful, an optimized structure at the ωB97-xD/aug-cc-pVDZ level of theory

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 191

was, however, obtained. The energy for the primary ozonide formation at this level of theory was -65.1 kcal mol-1 which only differs by 2 kcal mol-1 when comparing the single point energy obtained from this optimized geometry.

Despite the variations in the energies for the optimized geometry obtained at the different level of theories and basis sets, the single point energies obtained from these geometries are confined between -63.9 and -62.5 kcal mol-1.

Vayner et al. obtained the single point energy of -62 kcal mol-1 for the primary ozonide formation for the reaction between propene and ozone at the CCSD(T)/cc-pVTZ level of theory after the structure was optimised at the B3LYP/6-311G(d,p) level. Referring to Table A.4, the calculated single point energies do not deviate much from the value obtained by Vayner et al. even though these values are for a different system (i.e., ionic vs neutral systems). Furthermore, the basis sets employed for the geometry optimisations include the diffuse function unlike the basis set used by Vayner et al. where they did not utilise the diffuse basis sets in their calculation as they were investigating a neutral system. We were unable to obtain the single point energy using the function and basis set, CCSD(T)/aug-cc-pVDZ due to an internal, unresolved computational issue encountered when using this function and basis set for the system described above. While a single point calculation carried out with this theory and a diffuse function would have been an ideal model for our system however, the energy value for the formation of the primary ozonide obtained at the B3LYP/6-31+G(d,p) geometry is -59.8 kcal mol-1. This value underestimates the exothermicity by ca. 2 kcal mol-1 when compared to the single point energy calculated at the CCSD(T)/-cc-pVDZ level of theory. The B3LYP level of theory seems to be working well when using both the functions (diffuse and non- diffuse) when comparing the exothermicity obtained from a single point calculation at the CCSD(T)/-cc-pVDZ level.

192 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

A.3 Cartesian coordinates of optimised structures

Ozone O 0.00000 1.08368 -0.21649 O 0.00000 0.00000 0.43298 O 0.00000 -1.08368 -0.21649

1-Cyclohexene-1-carboxylic acid ozonolysis

1-Cyclohexene-1-carboxylic acid H -1.91153 1.01804 -1.46261 C -1.82760 1.17928 -0.37961 H -2.33384 2.12561 -0.15945 C -0.33965 1.28885 -0.00294 H 0.14887 1.97635 -0.70822 H -0.25049 1.74738 0.99500 C 0.35646 -0.06160 -0.01821 C 1.85434 -0.15219 -0.00291 C -0.32917 -1.21919 -0.03666 H 0.24284 -2.14345 -0.07407 C -1.82794 -1.31560 -0.00630 H -2.17360 -1.66235 -0.99299 H -2.12361 -2.10609 0.69580 C -2.50072 0.01609 0.35822 H -3.56988 -0.02320 0.12229 H -2.42142 0.17942 1.44149 O 2.48333 -1.17897 -0.13289 O 2.53519 1.01766 0.18094 H 1.93019 1.76498 0.28872

Complex C -0.45409 -0.22672 1.17277 C -0.87980 0.46491 0.08932 H -0.00848 0.30566 2.01105 C -0.73230 1.95823 0.01099 O 3.11486 -1.15187 -0.92747 O 2.79655 0.01712 -0.56206 O 2.23770 0.14104 0.58193 C -0.63725 -1.70904 1.34023 C -1.05697 -2.40645 0.03807 C -2.13694 -1.59316 -0.68802 C -1.62554 -0.19119 -1.04898 H -1.39416 -1.87370 2.12342 H 0.29066 -2.14136 1.73589 H -1.41244 -3.41956 0.25530 H -0.17989 -2.51228 -0.61464 H -3.01782 -1.49992 -0.03852 H -2.46700 -2.11123 -1.59492 H -2.44631 0.47043 -1.34527

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 193

H -0.95920 -0.24300 -1.92436 O -1.56965 2.66660 -0.50538 O 0.38191 2.50556 0.55701 H 1.04099 1.81790 0.75355

Product (DeMore) C -0.11356 -0.68659 0.62057 C -0.34925 0.57654 -0.13266 H 0.69873 -0.69737 1.35295 C 0.53158 1.77212 0.20107 O 0.35232 -0.54907 -0.73485 O 2.75705 -1.07345 -0.70829 O 2.98756 -1.67860 0.32930 C -1.22949 -1.67658 0.86008 C -2.40538 -1.49415 -0.11277 C -2.83241 -0.02187 -0.18083 C -1.71586 0.88693 -0.72456 H -1.57099 -1.53423 1.89457 H -0.81898 -2.69219 0.80030 H -3.24277 -2.11979 0.21443 H -2.11574 -1.84486 -1.11081 H -3.11463 0.31685 0.82535 H -3.72233 0.08992 -0.80961 H -1.94278 1.93619 -0.51996 H -1.63028 0.77506 -1.81288 O 0.06073 2.80630 0.61763 O 1.85317 1.60700 0.03813 H 2.05929 0.73463 -0.35500

Product (Criegee) C -0.31525 0.72014 -0.83241 C 0.41932 -0.05414 0.31826 O 1.22436 0.97162 0.94229 O 0.95457 2.21868 0.16107 O -0.38322 2.03388 -0.26819 H 0.33700 0.76493 -1.71273 C 1.33729 -1.12216 -0.30287 O 2.65193 -0.85658 -0.25908 O 0.89336 -2.12349 -0.81604 C -0.52596 -0.63180 1.39650 C -1.81167 -1.25227 0.83288 C -2.56638 -0.23497 -0.03129 C -1.70184 0.21527 -1.21589 H -2.19522 0.99698 -1.80439 H -1.54120 -0.63420 -1.89018 H -2.85535 0.63072 0.57822 H -3.49300 -0.67373 -0.41765 H -0.78363 0.20714 2.05139 H 0.02469 -1.35713 2.00469 H -2.43709 -1.57905 1.67127

194 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

H -1.57065 -2.14301 0.24196 H 2.77323 -0.00604 0.20594

1-Cyclohexene-1-Carboxyl ozonolysis

1-Cyclohexene-1-Carboxyl C 0.27863 1.20559 0.07577 C -0.39832 0.04732 0.00398 H -0.31127 2.11805 0.14360 C -1.94942 0.02854 -0.01620 C 1.78602 1.32382 0.06762 C 2.47456 0.01291 -0.34714 C 1.80102 -1.18582 0.33559 C 0.31997 -1.28463 -0.06255 H 2.14222 1.62603 1.06835 H 2.09495 2.13860 -0.60562 H 3.54832 0.05128 -0.11298 H 2.39052 -0.10876 -1.43717 H 1.87804 -1.06059 1.42656 H 2.32954 -2.11796 0.08802 H -0.21834 -1.99988 0.56799 H 0.23059 -1.69024 -1.08223 O -2.53167 1.14483 0.02805 O -2.46325 -1.12520 -0.07791

Complex (DeMore) C -0.27572 -0.39251 0.94825 C -0.47895 0.70112 0.17619 H 0.61037 -0.41700 1.57840 C 0.51240 1.85982 0.20787 O 1.23551 -1.20315 -1.07522 O 2.37699 -0.81984 -0.63088 O 2.87828 -1.53857 0.32373 C -1.21650 -1.56802 1.01658 C -2.24126 -1.56973 -0.12911 C -2.80859 -0.16063 -0.35383 C -1.69082 0.82940 -0.71616 H -1.74142 -1.55781 1.98760 H -0.63064 -2.49651 1.00378 H -3.04612 -2.28798 0.08041 H -1.74379 -1.90464 -1.04938 H -3.30779 0.17699 0.56670 H -3.57458 -0.17328 -1.14154 H -2.03945 1.86590 -0.66827 H -1.37067 0.66391 -1.75744 O 0.03396 3.01830 0.11275 O 1.73036 1.53498 0.33225

Complex (Criegee)

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 195

H 3.00990 -1.22251 -0.31627 C 2.57922 -0.65404 0.52196 H 3.23461 -0.82401 1.38749 C 1.16391 -1.17482 0.81792 H 1.13844 -2.26909 0.85128 H 0.83961 -0.83063 1.81057 C 0.14911 -0.72247 -0.20784 C -1.16009 -1.49777 -0.32427 C 0.41181 0.27569 -1.08636 H -0.33391 0.49746 -1.84478 C 1.69793 1.06197 -1.10885 H 2.27872 0.78437 -2.00580 H 1.46423 2.12894 -1.22204 C 2.54797 0.83612 0.15181 H 3.56456 1.22505 -0.00028 H 2.10628 1.40051 0.98369 O -1.32535 2.27169 -0.30726 O -1.90483 1.46530 0.51742 O -1.18121 1.09871 1.51669 O -2.16882 -0.81058 -0.67131 O -1.12499 -2.72988 -0.08430

TSa (DeMore) C -0.32649 -0.23831 -0.62919 C 0.78694 0.35986 -0.01980 H -0.92712 0.37674 -1.29619 C 1.08827 1.83327 -0.13800 O -1.52945 -0.20393 0.82395 O -2.54179 0.63438 0.57315 O -3.28116 0.27002 -0.48263 C -0.34923 -1.72148 -0.92564 C 0.45298 -2.53523 0.09889 C 1.85233 -1.93625 0.29420 C 1.76911 -0.47210 0.75928 H 0.07458 -1.87433 -1.93159 H -1.39250 -2.05061 -0.96167 H 0.52394 -3.58253 -0.22377 H -0.08374 -2.53064 1.05665 H 2.40159 -1.97737 -0.65699 H 2.42969 -2.52444 1.02010 H 2.75333 0.00880 0.72895 H 1.44536 -0.43628 1.81292 O 1.76700 2.02899 -1.18747 O 0.72683 2.62705 0.74964

TSb (Criegee) H 2.47495 -1.90296 -0.38238 C 2.25665 -1.23826 0.46717 H 2.87369 -1.58797 1.30632 C 0.76601 -1.33984 0.83233

196 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

H 0.43117 -2.38087 0.87920 H 0.60575 -0.91457 1.83221 C -0.13141 -0.62647 -0.15262 C -1.57588 -1.11284 -0.35244 C 0.36860 0.28587 -1.05420 H -0.29837 0.61387 -1.84571 C 1.82634 0.65553 -1.14275 H 2.24848 0.19538 -2.05289 H 1.91849 1.74027 -1.28287 C 2.62841 0.20155 0.08610 H 3.70548 0.29117 -0.11282 H 2.39705 0.86674 0.92790 O -0.33825 2.35964 -0.15283 O -1.28702 1.89490 0.61037 O -0.85111 1.06185 1.50200 O -2.35477 -0.24529 -0.83903 O -1.81749 -2.30541 -0.04183

Ozonolysis product (DeMore) C 0.16099 -0.59150 0.58562 C -0.40476 0.60093 -0.09416 H 0.99890 -0.38523 1.25717 C 0.21248 2.01325 0.24243 O 0.48359 -0.34138 -0.78331 O 2.83200 -0.75806 -0.87350 O 3.02733 -1.43826 0.14148 C -0.66326 -1.83298 0.85839 C -1.90220 -1.92547 -0.04702 C -2.66583 -0.59301 -0.06074 C -1.82512 0.55929 -0.64078 H -0.97704 -1.79723 1.91271 H -0.02924 -2.72299 0.74675 H -2.55225 -2.74112 0.29790 H -1.58698 -2.17515 -1.06833 H -2.95761 -0.34448 0.97109 H -3.59932 -0.69330 -0.63145 H -2.28284 1.53059 -0.43778 H -1.76266 0.46296 -1.73321 O -0.48812 2.98737 -0.13462 O 1.30460 1.98569 0.85277

Ozonolysis product (Criegee) H -0.31112 -2.51045 -0.22524 C -1.02231 -1.84763 -0.73470 H -1.51088 -2.44473 -1.51722 C -0.24647 -0.68449 -1.37230 H 0.52668 -1.06663 -2.04339 H -0.93548 -0.05475 -1.95054 C 0.44738 0.20171 -0.32410 C 1.79338 -0.46947 0.30808

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 197

C -0.50826 0.62764 0.80402 H 0.08186 1.10693 1.59003 C -1.41278 -0.46913 1.35410 H -0.77421 -1.09644 1.98902 H -2.16733 -0.01716 2.01117 C -2.06914 -1.33265 0.26504 H -2.59989 -2.17104 0.73756 H -2.82300 -0.73869 -0.26916 O -1.31276 1.61376 0.12406 O -0.34533 2.43189 -0.52259 O 0.81395 1.44297 -0.89316 O 2.18036 0.04895 1.37661 O 2.24159 -1.43295 -0.35030

3-Cyclohexene-1-carboxylic acid ozonolysis

3-Cyclohexene-1-carboxylic acid C -1.80309 1.26887 -0.31237 C -2.54651 0.21600 0.04961 C -1.96525 -1.13615 0.38101 C -0.49760 -1.26238 -0.05362 C 0.29354 -0.00123 0.32249 C -0.29588 1.23837 -0.39925 C 1.77667 -0.14520 -0.00470 O 2.23780 -0.94718 -0.77996 O 2.61154 0.73703 0.62074 H 0.19518 0.16239 1.40704 H -0.43675 -1.39980 -1.13878 H -0.03587 -2.14626 0.39737 H -2.56163 -1.92081 -0.10198 H -2.06227 -1.31995 1.46234 H 0.01826 1.23154 -1.45333 H 0.11343 2.16422 0.02682 H 2.11860 1.30593 1.22976 H -3.62826 0.32303 0.10847 H -2.28664 2.21128 -0.56297

Complex (DeMore) C -0.83222 -0.18465 -1.36481 C -1.27633 1.05042 -1.03022 H -1.40772 -0.79627 -2.05476 H -2.19794 1.42207 -1.47210 O -2.92575 0.30177 0.91966 O -3.30357 -0.82737 0.46045 O -2.38445 -1.69725 0.28824 C -0.50340 1.99006 -0.14397 C 0.63650 1.28940 0.60871 C 1.41547 0.35606 -0.32849 C 0.47874 -0.74915 -0.88124 C 2.62335 -0.26577 0.36821

198 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

O 2.80711 -0.26781 1.56041 O 3.53173 -0.87389 -0.45101 H 1.78727 0.94491 -1.18194 H 0.23072 0.69793 1.43558 H 1.31160 2.02664 1.05318 H -1.18625 2.46564 0.56960 H -0.10778 2.80953 -0.76465 H 0.28256 -1.49033 -0.09392 H 0.95796 -1.29939 -1.70166 H 3.27643 -0.78257 -1.38051

Complex (Criegee) C 0.93259 0.38459 1.36316 C 1.35983 1.35563 0.51267 O 2.93374 -0.10086 -1.02884 O 3.13048 -1.06454 -0.20855 O 2.07087 -1.64028 0.22370 H 1.55245 0.10669 2.21186 H 2.32262 1.82955 0.68371 C 0.51665 1.88289 -0.61676 C -0.95543 1.45349 -0.51373 C -1.06742 -0.03691 -0.11185 C -0.42359 -0.25819 1.26747 C -2.53515 -0.45353 -0.09380 O -2.98633 -1.13704 -1.18282 O -3.30206 -0.17967 0.79844 H 0.94825 1.53810 -1.56727 H 0.58263 2.97810 -0.63939 H -1.46531 1.63803 -1.46603 H -1.47259 2.05042 0.24641 H -0.51685 -0.63691 -0.84907 H -0.34064 -1.32985 1.4806 H -1.08770 0.15497 2.03906 H -2.26136 -1.31779 -1.79851

Ozonolysis product (DeMore) C -1.04505 -0.48731 -0.30528 C -1.34034 0.93696 -0.55568 H -1.75058 -1.22897 -0.69478 H -2.24289 1.17953 -1.11658 O -1.61998 0.32813 0.72755 O -3.89127 -0.32186 0.63867 O -3.94885 -1.19723 -0.22377 C -0.23315 1.96509 -0.56610 C 1.04365 1.46772 0.12964 C 1.44468 0.07939 -0.39236 C 0.36774 -0.98719 -0.04893 C 2.79704 -0.36202 0.16452 O 3.30078 0.07728 1.16833 O 3.43418 -1.34876 -0.53125

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 199

H 1.52870 0.13495 -1.48931 H 0.89414 1.41504 1.21193 H 1.85882 2.17736 -0.03959 H -0.59068 2.88752 -0.09323 H -0.02153 2.21279 -1.61606 H 0.44629 -1.26610 1.00859 H 0.52958 -1.90060 -0.63229 H 2.94175 -1.58781 -1.32986

Ozonolysis product (Criegee) C 1.16722 -0.80953 0.54453 C 1.64833 0.65507 0.63953 O 2.95601 0.61518 0.04915 O 3.07639 -0.74944 -0.56010 O 1.72953 -1.18193 -0.72059 H 1.64961 -1.41081 1.32442 H 1.76723 0.94562 1.69075 C 0.76427 1.64411 -0.13222 C -0.73063 1.42575 0.13477 C -1.14159 -0.01197 -0.26533 C -0.33882 -1.03883 0.55105 C -2.63719 -0.20418 -0.01625 O -3.45853 -0.01397 -1.08464 O -3.11034 -0.46691 1.06340 H 0.97290 1.51533 -1.19991 H 1.05567 2.66732 0.12723 H -1.31614 2.16327 -0.42558 H -0.96850 1.57537 1.19591 H -0.92541 -0.14811 -1.33369 H -0.53870 -2.05905 0.20609 H -0.68312 -0.99148 1.58980 H -2.94764 0.15665 -1.88922

3-Cyclohexene-1-carboxyl ozonolysis

3-Cyclohexene-1-carboxyl C 1.87136 1.20121 -0.16677 C 2.53347 0.04142 -0.03584 H 2.44531 2.12607 -0.25992 H 3.62490 0.03878 -0.04167 C 1.82952 -1.28600 0.12620 C 0.34442 -1.11022 0.48771 C -0.34263 -0.03790 -0.37966 C 0.36764 1.31196 -0.19718 C -1.87801 0.01389 -0.04564 O -2.24725 0.89782 0.77579 O -2.57307 -0.86905 -0.61839 H -0.25703 -0.35646 -1.42852 H 0.26325 -0.80955 1.54236 H -0.19188 -2.05945 0.37923

200 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

H 2.34287 -1.88363 0.89577 H 1.92294 -1.86560 -0.80762 H -0.01132 1.77070 0.72748 H 0.06899 2.00282 -0.99924

Complex (DeMore) C -0.56284 -0.40435 -0.06549 C -0.80880 0.91383 -0.07581 H -1.40542 -1.09764 -0.10538 H -1.83959 1.26502 -0.11961 O -5.07207 0.36141 0.51257 O -4.38426 -0.20133 -0.42526 O -3.85656 -1.34571 -0.15962 C 0.28118 1.95788 -0.02827 C 1.63984 1.35449 0.37734 C 1.90499 0.03484 -0.36302 C 0.82569 -0.99621 -0.00695 C 3.36498 -0.49034 -0.00880 O 3.48566 -1.02863 1.11558 O 4.21465 -0.25999 -0.90640 H 1.89239 0.22694 -1.44217 H 1.64781 1.15417 1.45624 H 2.44557 2.07003 0.17388 H -0.00102 2.75897 0.67109 H 0.36595 2.44318 -1.01429 H 1.03803 -1.38926 0.99683 H 0.88670 -1.85815 -0.68563

Complex (Criegee) C 0.77970 -0.06321 1.32059 C 1.19863 1.11503 0.79507 O 3.40476 0.32638 -0.76143 O 3.43153 -0.87500 -0.27110 O 2.33048 -1.54111 -0.36842 H 1.41677 -0.57030 2.04395 H 2.14717 1.54107 1.11523 C 0.38422 1.88564 -0.20670 C -1.09563 1.45299 -0.21363 C -1.23842 -0.07801 -0.21589 C -0.56306 -0.67163 1.02720 C -2.77287 -0.45631 -0.29704 O -3.36147 -0.58549 0.80809 O -3.22430 -0.54209 -1.46675 H 0.82260 1.72386 -1.20344 H 0.47567 2.96394 -0.00891 H -1.60528 1.87134 -1.08855 H -1.59863 1.85276 0.67762 H -0.75896 -0.46730 -1.12131 H -0.45804 -1.75957 0.92568

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 201

H -1.24476 -0.52439 1.87905

TSa (DeMore) C 1.10810 0.05906 0.49688 C 1.06824 1.45373 0.34220 H 1.83214 -0.35702 1.21405 H 1.99479 2.00216 0.50474 O 2.20868 -0.19072 -0.86084 O 3.49059 -0.32072 -0.39237 O 3.58859 -1.24138 0.56747 C -0.14174 2.22076 -0.05656 C -1.31557 1.32375 -0.48879 C -1.42488 0.07308 0.39374 C -0.14308 -0.76736 0.26671 C -2.73911 -0.72862 0.02002 O -2.57795 -1.82451 -0.57074 O -3.79925 -0.13603 0.34972 H -1.55700 0.40079 1.43558 H -1.16784 1.01117 -1.53183 H -2.25575 1.88060 -0.44546 H 0.12719 2.96742 -0.82158 H -0.44612 2.82113 0.82129 H -0.12454 -1.21608 -0.73237 H -0.16000 -1.60953 0.96438

TSb (Criegee) C 0.89139 -0.28969 1.20959 C 1.31049 0.97164 0.86411 O 3.10787 0.42703 -0.76650 O 3.26809 -0.82015 -0.41753 O 2.16818 -1.51403 -0.44505 H 1.50117 -0.86762 1.90107 H 2.21644 1.37352 1.30998 C 0.47857 1.87771 0.00147 C -1.00880 1.47135 -0.01216 C -1.18382 -0.03886 -0.24190 C -0.46621 -0.82507 0.86139 C -2.72604 -0.37656 -0.29965 O -3.25202 -0.71361 0.79584 O -3.25519 -0.22764 -1.42925 H 0.87944 1.83411 -1.02252 H 0.60231 2.91852 0.33365 H -1.54067 2.02379 -0.79413 H -1.47204 1.74016 0.94744 H -0.75560 -0.28966 -1.21921 H -0.38554 -1.88607 0.59422 H -1.11454 -0.80267 1.75246

Ozonolysis product (DeMore)C -1.04860 -0.42884 -0.35543 C -1.29860 1.02283 -0.27776

202 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

H -1.80270 -1.02883 -0.88764 H -2.19964 1.41345 -0.75279 O -1.59986 0.14819 0.84072 O -3.89212 -0.33654 0.49907 O -3.87902 -0.94493 -0.59055 C -0.15348 1.98761 -0.07029 C 1.12612 1.29174 0.42944 C 1.45470 0.04103 -0.40430 C 0.35227 -1.02016 -0.26713 C 2.88514 -0.51372 -0.01672 O 2.92728 -1.57517 0.65037 O 3.82911 0.21532 -0.42472 H 1.52477 0.35679 -1.45550 H 1.00442 1.00588 1.48214 H 1.97072 1.98522 0.37484 H -0.47095 2.78542 0.61666 H 0.04490 2.46707 -1.04063 H 0.47758 -1.54367 0.68671 H 0.46235 -1.77916 -1.04975

Ozonolysis product (Criegee) C 1.11885 -0.84017 0.44071 C 1.56404 0.62037 0.67027 O 2.92147 0.64768 0.17999 O 3.12461 -0.68097 -0.48951 O 1.80394 -1.12224 -0.79506 H 1.56731 -1.48297 1.21058 H 1.60170 0.82839 1.74788 C 0.70613 1.64596 -0.07362 C -0.79207 1.39213 0.15094 C -1.21266 0.00287 -0.36039 C -0.38305 -1.08687 0.33049 C -2.75576 -0.19650 -0.10452 O -3.06874 -0.72854 0.99602 O -3.50405 0.24094 -1.01625 H 0.93710 1.56649 -1.14238 H 0.99932 2.65517 0.24553 H -1.38258 2.15826 -0.36275 H -1.03638 1.46868 1.22143 H -1.05586 -0.02296 -1.44568 H -0.53797 -2.06235 -0.14647 H -0.78328 -1.19033 1.34706

Propenoate ozonolysis

TS(Criegee) C -0.56154 0.77892 -0.59386 C -1.53575 -0.13484 0.12704 C 0.24742 1.63505 0.09671 O 2.19262 0.34823 0.43202

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 203

O 1.67191 -0.81802 0.18939 O 1.23265 -0.94080 -1.02346 O -2.66950 -0.25879 -0.40124 O -1.09558 -0.64758 1.19416 H -0.60737 0.81698 -1.67874 H 0.19733 1.66174 1.18027 H 0.85244 2.38221 -0.40784

TS(DeMore) C -0.40838 1.09695 0.19126 C 0.92362 0.86107 -0.35398 H -0.63136 0.61295 1.15107 C 1.81861 -0.28571 -0.02805 O -1.41051 0.53765 -0.76746 O -2.04100 -0.65416 -0.26446 O -2.67469 -0.41319 0.89265 O 2.81034 0.17365 0.61508 O 1.55565 -1.44771 -0.37335 H 1.33228 1.59462 -1.04937 H -0.66383 2.16794 0.23361

β-lactone C 0.07378 -0.26318 0.44562 C 1.58239 -0.01274 0.00143 C -0.58858 1.05474 0.02057 O -2.06150 0.59277 0.33888 O -2.13616 -0.58575 -0.37859 O -0.64453 -1.26683 -0.20250 O 1.67272 1.19127 -0.34136 O 2.48116 -0.87083 0.09601 H 0.01083 -0.37044 1.53778 H -0.52782 1.25585 -1.09296 H -0.37817 1.95664 0.65001

204 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

Appendix B

- - B.1 Kinetic plots of IO + O3 and IO2 + O3 reactions

- Figure B.1: (a) The kinetic plot for the reaction IO + O3. The exponential fit for the decay of m/z 143 is given. (b) The ln plot for the decay of m/z 143. The straight line fit does not correlate with the data well.

- Figure B.2: (a) The kinetic plot for the reaction IO2 + O3. The exponential fit for the decay of m/z 159 is given. (b) The ln plot for the decay of m/z 159. The gradient of the straight line fit indicates the pseudo-first order rate constant.

Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry 205

B.2 Cartesian coordinates of optimised structures

Optimised transition states at the UCCSD/6-311+G(df) level of theory

[BrO.OOO]- TS O -1.80466 0.77267 -0.58238 Br -0.72293 -0.32786 0.09562 O 2.33296 -0.56334 -0.45927 O 1.83723 0.66826 -0.16756 O 0.79728 0.55683 0.79088

- [BrO2.OOO] TS O 1.22354 1.31523 0.54041 Br 0.82388 -0.06141 -0.20952 O 0.62808 -1.27003 0.84037 O -0.94257 0.11265 -0.96745 O -2.00304 -0.40566 -0.16190 O -2.51048 0.51647 0.66

206 Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

207