CHARACTERISATION OF OZONOLYSIS REACTIONS RELEVANT … · ii Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry ABSTRACT Ozone plays

CHARACTERISATION OF OZONOLYSIS

REACTIONS RELEVANT TO ATMOSPHERIC

CHEMISTRY 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

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

ABSTRACT

Ozone plays a significant role in the chemistry of the lower (troposphere) and

upper (stratosphere) 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 aerosol. Detailed

understanding of many of these fundamental ozonolysis reactions in the gas phase 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 bromide). 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 electrospray 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-carbon double bond 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

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

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-atom addition to Br- were

lower than the initial addition to form BrO- ion.

Finally, the real time molecular analysis of ozone derived secondary organic

aerosols 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.

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

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 Halogens 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

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

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

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

2.1 Ion-molecule 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 concentration 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

carboxylic acid ozonolysis ............................................................................... 106

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

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 paper analysis ............................................................................. 155

5.3.6 Online analysis of 1-cyclohexene carboxylic acid ozonolysis ......................... 156

5.3.7 Particle concentration and variability in ozone concentrations ........................ 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

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

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

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

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 Ozonide

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

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

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, Antarctica 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 alkenes 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 dioxirane……………………………………...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 aldehyde; 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 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. 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

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

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

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

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 voltages (8kV) and using

oxygen 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 voltage………………………………………….80

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

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)

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

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-

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

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 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…………………………………………………………………… 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

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

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

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

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

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

LIST OF SCHEMES

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……………………………………………………………30

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 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 ozonides (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 iodine 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

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

xviiiCharacterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry

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

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

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

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

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 spectroscopy 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.

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

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.

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

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.

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

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 Earth 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, transport, lifetimes and fates of certain

anthropogenic (man-made) and biogenic (natural) chemicals are examples of such

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

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.,

smog episodes in polluted regions) and on a global scale2 (e.g., affecting the radiative

forcing 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 ozone layer 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 altitudes 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 atoms initiates the free

radical chemistry of the stratosphere, through reactions with water, methane and

nitrous oxide for instance. The singlet oxygen 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


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 photodissociation.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 nitrous

oxide as indicated in Equations (1.6-1.10).8 Subsequently, the reactions of these

oxides 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)


+ → + (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 chlorine, 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 leads 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

losses.1 In this processes, atomic chlorine reservoir species such as HCl and ClONO2

react rapidly on ice surfaces generating Cl2 and HNO3.12

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.


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 hydroxyl radical (OH), nitrate radical (NO3) or

ozone (O3) undergo chemical transformation.1 Such reactions can result in products

of low vapour pressure (lower volatility) that can partition between the vapour and

liquid phases by either condensing on pre-existing particles or forming a critical

nucleus upon which other gases can condense.14 The first oxidation steps lead to an

array of compounds which generally include polar oxygenated functional groups

such as aldehydes, ketones, alcohols, nitrates, peroxyacyl nitrates, carboxylic acids,


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 greenhouse gas in the

upper troposphere. Ozone in the troposphere is thought to be formed from the

photolysis of NO2 (Reaction1.14).18 Although a fraction of total NO2 emitted into the

troposphere is via combustion 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

tropospheric ozone.10


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 hydrogen from the

organic compound 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

formed from VOC-NOx reactions in air depends critically on the NO concentration.4

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


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 haze 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).


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.


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


+ → + (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

atoms (H2CO5) (~-47 kcal mol-1).27 Ultimately, the compound dissociates into

formic acid and triplet oxygen. 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


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


organic compounds which represent about 10% of the total biogenic hydrocarbon

emissions.17 They consist of two isoprene 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 glass 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

particles where aerosol seed particles such as MgSO4 or (NH4)2SO4 are utilized.35,36

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 organic matter in


PM2.5 (i.e., particles less than 2.5 µm in diameter).40 In 2010, it was reported that in

Hong Kong, FA were the major component (46-80% by weight) of extractable

organic compounds in PM2.5 of ambient aerosols41. Huang et al., reported seasonal

average concentration of FA at 260-483 ng m-3 in PM2.5 where unsaturated FA being

present at a lower concentration than saturated FA in Beijing, 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


O

R R'O

O O

O

O

RR'

HR''

a) Dipolar Cycloadditions

i)

ii)O

O

H

R OO

H

R'

O O

O OH

RR'

H

b) Addition to an acid

R''

H

OH

R O

O

HO R'

O

O

OH

OR'

HR +CI''

Polymer

O

R O

O

R'

-H2Oacyloxyalkyl

hydroperoxide (AAHP)

c) Addition of AAHP to an aldehyde

O

O

OH

OR'

HR O

H R''

O

OR' OO

HOHR''

R

O

OR' OO

HOHR''

R

peroxyhemiacetal

O

HO R'''

O

OR' OO

HOR''

RO

R'''d) Reaction of a peroxyhemiacetal with an acid

e) Ketone/Aldehyde formation

H

R R'

HO

H

R'' O

O

HR'

O

CH2R'R

O

R'RH2C

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%


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 halogen

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).


+ ( ) → + ( ) (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 salt 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

heteroatoms are included, this value rises to over 1 million C10 isomers.50

Traditionally, the analysis of such convoluted systems generally incorporated off-line

methods and recently, on-line methods have revolutionised atmospheric chemical

analysis.


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.


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 solid, 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, protonation, 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 volts to

bombard aluminium 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 anode 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.


+ → • + 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 molecules 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 plasma through a series of cascading chemical

reactions. A pathway in chemical ionisation which generates a positive ion, M+H+


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

conditions, mixtures of CH4/H2O results in abundant m/z 17 ions, [H3O]+ .58

Attachment of the ion to an analyte can also result in ion formation for

instance the presence of [M+NH4]+ ions observed when using ammonia 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


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.


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 density 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


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.


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.


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


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-


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).


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.


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


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


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.


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

and H2 to form H3+.79 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 papers 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 acetaldehyde

(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


(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).


(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 methanol to formaldehyde 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.


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,


(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. (Stainless Steel)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).


Fig

ure

2.1

: S

chem

atic

of

the

mod

ifie

d T

herm

o S

cien

tifi

c L

TQ

XL

line

ar io

n-tr

ap m

ass

spec

trom

eter


Fig

ure

2.2

: P

hoto

grap

h of

the

ozon

e-m

ixin

g m

anif

old


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.


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


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.

The ozone concentration is displayed either in g N-1m-3 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.


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.


Figure 2.6: The current layout of the ozone mixing manifold, the LTQ mass

spectrometer and the ozone trolley in the laboratory.


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 death.

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 corona discharge 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


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)


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 dipole 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 rate equation. 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 = x100% (2.6)


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.


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.


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


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-life 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

ozone (1.0 ± 0.25 × 10-11 cm3 molecule-1 s-1) , 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


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.


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


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.

y = 1E+08xR² = 0.9958

0

5E+09

1E+10

1.5E+10

2E+10

2.5E+10

3E+10

0 50 100 150 200 250 300

Inte

rnal

O3

conc

entr

atio

n (m

olec

/cm

3 )

External O3 concentration (g/Nm3)


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

Nm-3 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.


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.


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 lightning 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.


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 climate change.15


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


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.


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.


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


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.


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

the I2 back to iodide ions (Equations 2.7 and 2.8).110 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.


+ 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.


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.


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


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 ethylene 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


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 acetylene 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

carbons 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

yield an oxirane and 1O2.127 The formation of 1,2-epoxy-3-butane from the

ozonolysis of 1,3-butadiene 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


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.


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


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).


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.


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 propene 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.


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.


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.


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


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.


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

Compound k1=k2[O3] (s-1) k2 (× 10-12 cm3 molecule-1 s-1) [ф%]a

[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.


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


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

hydroperoxyl groups although 1-4 hydrogen shifts are not common.145 The resultant

loss of the hydrogen peroxide 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


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

alkene during ozonolysis is through epoxidation by O3.149

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.


OO

OOO

O

O-

OOO

O

O-

m/z 125

OzonolysisO

O

O- O

OO

O

O- OH

O

O

O

O-

OO

O

OH

O

-OH

H-Shift

H-Shift

e-

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


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


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.

From TSD1, an epoxide and a singlet oxygen complex is formed, Prod (D2 + 1O2).

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

products (Prod (D1 + 1O2)) is 6.4 kcal mol-1.

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

formation of the epoxide and 1O2 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.


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

transition state (TSD3) which sits energetically 13.7 kcal mol-1 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.


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


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


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

hydrogens 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 oxygens 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.


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.


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


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.


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

the comparison of the atmospheric lifetimes (where lifetime s-1 = 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


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

(corresponding to 2.64 × 1010 molecule cm-3 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

OH and NO3 is similar to the removal by O3.143 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.


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

charge transfer mechanism from O3-.165

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 phytoplankton is thought to involve

several enzymatic processes and the haloform reaction.167,168 These volatile

compounds have low solubility and are subsequently degassed into the atmosphere

and are broken down by sunlight forming active iodine.


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

molecule s-1.77 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

Br atoms and O3- in the solution phase.173

+ → + (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


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


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


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

240 g Nm-3 (“High” O3) and 12 g/Nm-3(“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.


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


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.


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).


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


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-


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

between I- and O3 (240 g Nm-3 vs 12 g Nm-3 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

between IO2- and O3.77 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


the Appendix). Therefore, the calculated upper limit for the second order rate

constant for the reaction of iodite ion (IO2-) with ozone is 1.95 ± 0.02 × 10-8 cm3

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

electron transfer pathway producing the O3- ion.173 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.


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).


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.

I- + O3 IO- + O2

IO- + O3 IO2- + O2

IO2- + O3 IO3

- + O2

k1

k2

k3

k1 k-1>>k-1

k-2k2 k-2>>

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


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


the singlet and triplet states. The geometric parameters for the structures are given in

Table 4.1. The experimental data for the bond lengths and bond angles for 1O3, 3O2

and BrO- is also included and there is excellent agreement between the experimental

values and theory. The largest difference was for the bond length of 3O2 where the

predicted value is smaller by 0.01Å. The Br-O bond distance for 3BrO- is greatly

exaggerated compared to other Br-O bond distances for 3BrO2- and 3BrO3

-. 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-

311+G(d,p)

Experiment

1O3 r(O-O) 1.245 1.27276 ± 0.00015180

θ(O-O-O) 118 116.7542 ± 0.0025180

1O2 r(O-O) 1.205

1BrO- r(Br-O) 1.809 1.814 ± 0.009181

1BrO2- r(Br-O) 1.707

θ(O-Br-O) 111.8

1BrO3- r(Br-O) 1.628

θ(O-Br-O) 107

Dihedral θ(O-Br-

O-O)

-114.7

3O3 r(O-O) 1.283

θ(O-O-O) 129.1

3O2 r(O-O) 1.198 1.2075182

3BrO- r(Br-O) 2.575

3BrO2- r(Br-O) 1.805

θ(O-Br-O) 158.4

3BrO3- r(Br-O) 1.649, 1.760

θ(O-Br-O) 106.1,147.7

Dihedral θ(O-Br-

O-O)

180


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

angle for 1BrO2-.

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

expected for the bond angle for 1BrO2-.

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


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.


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.


4.4 Conclusion


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

could not be determined for the reactions between IO- and IO2-, the 2nd 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.


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

the lack of 2nd 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

surface shows that the formation of the products 1BrO2- and 1O2 from 1BrO- + 1O3

proceeds via a transition state which is about 8 kcal mol-1 lower in energy compared

the transition state which results in the formation of 1BrO3- and 1O2 from 1BrO2

- and 1O3. However, the products 1BrO3

- and 1O2 sit at a deeper well at -140.4 kcal mol-1

compared to the products from the other channel. The products from the BrO- + 1O3


reaction channel is found at 30.2 kcal mol-1 below the entrance channel. As this

energy is more than the activation energy required for the formation of 1BrO3- and

1O2, initial formation of the 1BrO2- and 1O2 is exothermic enough to surmount this

barrier to produce the highly stable 1BrO3- 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, ozone depletion 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


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

NO2 in the consumption of ozone has not been studied.186 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.


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


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


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


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.


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

agent, sodium thiosulfate (Na2S2O3) and potassium iodide (KI) in water.110 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


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

condense. 197 The major peaks are separated by 14 (CH2) and 16 (O) Dalton

differences and are indicative of an aerosol mass spectrum (Figure 5.4).


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).


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.


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

C10H15O3-.108 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


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


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-

double bond under low NOx (i.e., low NO + NO2).206 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


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.


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


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


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.


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


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.


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.


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


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.


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


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.


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.


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.


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

high capillary voltages. 101 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.


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-

and O3 are exothermic by 30.2 and 140.4 kJ mol-1. The barrier for the 2nd and 3rd 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


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 mining tools.


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


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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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


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 single

bond (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

(A)

r2 (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


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


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.

Theory/Basis Set

r1 (Å) O-O-O

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


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


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.


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.

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

-80

-75

-70

-65

-60

-55

-50

-45

-40B3LYP M062X WB97XD CAM-B3LYP

Ener

gies

in k

cal/

mol

Levels of theory

6-31G(d)

6-311G(d,p)

6-31+G(d)

6-31+G(d,p)

6-31++G(d)

6-31++G(d,p)

6-311+G(d,p)

6-311++G(d,p)

aug-cc-pVTZ


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


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-pVDZ

-65.1 -63.1

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


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.


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


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


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)


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


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


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


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


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


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


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


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


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


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.


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

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CHARACTERISATION OF OZONOLYSIS REACTIONS RELEVANT … · ii Characterisation of ozonolysis reactions relevant to atmospheric chemistry using mass spectrometry ABSTRACT Ozone plays