experimental and computational studies of the unimolecular
TRANSCRIPT
University of Wollongong Thesis Collections
University of Wollongong Thesis Collection
University of Wollongong Year
Experimental and computational studies
of the unimolecular rearrangements of
sulphonated azo dyes and phenoxide
anions in the gas-phase
Aravind RamachandranUniversity of Wollongong
Ramachandran, Aravind, Experimental and computational studies of the unimolecularrearrangements of sulphonated azo dyes and phenoxide anions in the gas-phase, Master ofScience - Research thesis, School of Chemistry, Faculty of Science, University of Wollongong,2008. http://ro.uow.edu.au/theses/2625
This paper is posted at Research Online.
Experimental and Computational Studies of
the Unimolecular Rearrangements of
Sulphonated Azo Dyes and Phenoxide
Anions in the Gas-Phase
A thesis submitted in fulfilment of the requirements for the award of the degree
MASTER OF SCIENCE (RESEARCH)
from
UNIVERSITY OF WOLLONGONG
by
Aravind Ramachandran
School of Chemistry, Faculty of Science
2008
CERTIFICATION
I, Aravind Ramachandran, declare that this thesis, submitted in fulfilment of the requirements for the award of Master of Science (Research), in the Faculty of Science, University of Wollongong, is wholly my work unless otherwise referenced or acknowledged. The document has not been submitted for qualifications at any other academic institutions. Aravind Ramachandran April 14, 2008
i
TABLE OF CONTENTS TABLE OF CONTENTS_________________________________________________________ I
LIST OF FIGURES____________________________________________________________ III
LIST OF TABLES______________________________________________________________ V
LIST OF SCHEMES ___________________________________________________________ VI
ABSTRACT ________________________________________________________________ VIII
ACKNOWLEDGEMENT ________________________________________________________ X
CHAPTER ONE: INTRODUCTION ________________________________________________ 1
1.1 IONIZATION TECHNIQUES _____________________________________________________ 2
1.2 TANDEM MASS SPECTROMETERS _______________________________________________ 7
1.3 ELUCIDATION OF GAS PHASE FRAGMENTATION MECHANISMS BY MASS SPECTROMETRY AND COMPUTATIONAL STUDY _______________________________________________________ 11
1.4 IDENTIFICATION OF TWO UNUSUAL ANION REARRANGEMENT IN THE GAS- PHASE____________ 18
1.5 COMPUTATIONAL METHODS__________________________________________________ 20
1.5.1 Basis set ___________________________________________________________ 21
1.5.2 Theoretical model ____________________________________________________ 23
REFERENCES FOR CHAPTER ONE_________________________________________________ 25
CHAPTER TWO: EVIDENCE OF AN INTRAMOLECULAR NUCLEOPHILIC AROMATIC SUBSTITUTION: AN EXPERIMENTAL AND THEORETICAL STUDY OF THE GAS-PHASE REARRANGEMENT OF AZO DYES______________________________________________ 28
ABSTRACT _________________________________________________________________ 28
2.1 INTRODUCTION ___________________________________________________________ 30
2.2 RESULTS AND DISCUSSION __________________________________________________ 34
ii
2.2.1 Collision induced dissociation (CID) of deprotonated azo dyes _________________ 34
2.2.2 Solution phase labelling _______________________________________________ 38
2.2.3 Evidence towards the mechanism for N2 loss ______________________________ 41
2.2.3.1 Positive ion experiment ___________________________________________________ 41
2.2.3.2 Dianion Experiment ______________________________________________________ 42
2.2.3.3 Authentic product experiment ______________________________________________ 44
2.2.3.4 Change of nucleophile____________________________________________________ 50
2.2.3.5 CID of Substituted analogues ______________________________________________ 52
2.2.3.6 Electronic structure calculation _____________________________________________ 54
2.3 CONCLUSION ____________________________________________________________ 70
2.4 EXPERIMENTAL___________________________________________________________ 71
2.4.1 Mass spectrometry ___________________________________________________ 71
2.4.2 Synthesis of azo compounds ___________________________________________ 71
2.4.3 Synthesis of authentic amine compounds _________________________________ 72
2.4.4 Calculations ________________________________________________________ 72
REFERENCES FOR CHAPTER TWO ________________________________________________ 74
CHAPTER THREE: COMPUTATIONAL INVESTIGATION OF THE REARRANGEMENT AND FRAGMENTATION OF PHENOXIDE ANION IN THE GAS-PHASE _____________________ 76
ABSTRACT _________________________________________________________________ 76
3.1 INTRODUCTION ___________________________________________________________ 78
3.2 MATERIALS AND METHODS __________________________________________________ 85
3.3 RESULTS AND DISCUSSION __________________________________________________ 86
3.4 CONCLUSION ___________________________________________________________ 108
REFERENCES FOR CHAPTER THREE ______________________________________________ 109
APPENDIX-1 _______________________________________________________________ 111
APPENDIX-2 _______________________________________________________________ 112
APPENDIX-3 _______________________________________________________________ 153
iii
LIST OF FIGURES Fig-1.1: Components of a basic mass spectrometer ___________________________________ 2
Fig-1.2: Schematic of the electrospray ionization process ______________________________ 5
Fig-1.3: Components of a tandem in space mass spectrometer__________________________ 8
Fig-1.4: Cross section of a linear ion trap __________________________________________ 10
Fig-1.5: The MS/MS spectrum of the 3-methyl- 2,3 epoxybutoxide anion__________________ 15
Fig-1.6: MS/MS spectrum of the 2,2-dimethyloxetan-3-olate ___________________________ 16
Fig-1.7: Reaction coordinate diagram of the Payne rearrangement ______________________ 17
Fig-2.1: Range of azo compounds________________________________________________ 32
Fig-2.2: CID Spectrum of the azodye 4-amino-3-(phenyldiazenyl)naphthalene-1-sulfonic acid as
shown in Fig-2.1(a) _______________________________________________________ 35
Fig-2.3: CID mass spectrum of the mass selected product ion at m/z 262 _________________ 37
Fig-2.4: CID mass spectrum of the mass selected product ion at m/z 298 _________________ 38
Fig-2.5: MS spectrum of deuterium labeled sample __________________________________ 39
Fig-2.6: CID mass spectrum of completely deuterium exchanged sample _________________ 40
Fig-2.7: CID mass spectrum of the positive ions of the azodye 4-amino-3-(phenyldiazenyl)
naphthalene-1-sulfonic acid as in (Fig-2.1(a))___________________________________ 41
Fig-2.8: CID mass spectrum of [M-2H]2- ions from the azo dye 4-amino-3-((4sulfophenyl)diazenyl)
naphthalene-1-sulfonic acid as in Fig-2.1(e) ____________________________________ 43
Fig-2.9: Comparision of MS/MS spectra of the secondary amine product with that of the MS3
spectrum of the azo dye anion, 4-amino-3-(phenyldiazenyl)naphthalene-1-sulfonate (Fig-
1(a)) ___________________________________________________________________ 46
Fig-2.10: Comparision of MS/MS spectra of the amine product with that of the MS3 spectrum of
the dianions from 4-amino-3-((4-sulfophenyl)diazenyl)naphthalene-1-sulfonic acid (Fig-
2.1(e))__________________________________________________________________ 47
Fig-2.11: Comparision of MS/MS spectra of the monoanions from disubstituted amine product
with that of the MS3 spectrum of the monoanions from 4-amino-3-((4-sulfophenyl)diazenyl)
naphthalene-1-sulfonic acid (Fig-2.1(e)) _______________________________________ 50
iv
Fig-2.12: CID mass spectrum of negative ions from 4-hydroxy-(phenyldiazenyl) naphthalene-1-
sulfonic acid (Fig-1(f)) _____________________________________________________ 51
Fig-2.13: CID mass spectrum of negative ions from 4-amino-3-((4-nitrophenyl)diazenyl)
naphthalene-1-sulfonic acid (Fig-1(c)) ________________________________________ 53
Fig-2.14: CID mass spectrum of negative ions from 4-amino-3-((4-methoxyphenyl)diazenyl)
naphthalene-1-sulfonic acid (Fig-1(b)) ________________________________________ 54
Fig-2.15: Structures of the Tautomer (1M1) and Meisenheimer transition state (TS1) on the 4-
amino-3-(phenyldiazenyl)benzene-1-sulfonate potential energy surface optimized at
B3LYP/6-31+G(d) level of theory_____________________________________________ 57
Fig-2.16: Reaction coordinate diagram for the intramolecular rearrangement of the model diazo
anion, 4-amino-3-(phenyldiazenyl)benzene-1-sulfonate model system calculated at
B3LYP/6-31+G(d) level of theory_____________________________________________ 60
Fig-2.17: Reaction coordinate diagram for the intramolecular rearrangement of the 4-hydroxy-
(phenyldiazenyl)benzene-1-sulfonate model system calculated at B3LYP/6-31+G(d) level of
theory __________________________________________________________________ 66
Fig-3.1: CID Mass Spectrum of the labeled ethoxide anion (Ph16O(CH2)218O-) _____________ 83
Fig-3.2: Reaction coordinate diagram for the fragmentation of the phenoxide anion in the gas-
phase calculated at B3LYP/6-311++G(d,p) level of theory _________________________ 88
Fig-3.3: Structures of the stationary points on the phenoxide potential energy surface optimized
at B3LYP/6-311++G(d,p) level of theory _______________________________________ 91
Fig-3.4: Potential energy diagram showing the involvement of benzene-oxide and oxepin
structures in the fragmentation of phenoxide calculated at B3LYP/6-311++G(d,p) level of
theory __________________________________________________________________ 95
Fig-3.5: Structures of the stationary points on the benzene-oxide and oxepin potential energy
surface optimized at B3LYP/6-311++G(d,p) level of theory ________________________ 98
Fig-A_2.1:Structures of the stationary points on the 4-amino-3(phenyldiazenyl)benzenesulfonate
potential energy surface optimized at B3LYP/6-311++G(d,p) level of theory __________ 130
v
LIST OF TABLES Table-2.1: Optimized stationary points calculated for the loss of N2 from 4-amino-3-
(phenyldiazenyl)benzenesulfonate anion ______________________________________ 61
Table-3.1: Optimized stationary points calculated for the loss of CO from phenoxide anion __ 107
Table-A_1.1: Tandem mass spectra of [M-H+]- Ions from azo dyes anions para substituted phenyl
and sulphonic acid analogues. _____________________________________________ 111
Table-A_2.1: The Cartesian coordinates for all the stationary points for the fragmentation of 4-
amino-3(phenyldiazenyl)benzenesulfonte calculated at B3LYP/6-31+G(d) level as illustrated
in Figure-2.16. __________________________________________________________ 112
Table-A_2.2: Optimized stationary points calculated for the loss of N2 from 4-hydroxy-3-
(phenyldiazenyl)benzenesulfonate Anion _____________________________________ 131
Table-A_2.3: Optimized stationary points calculated for the loss of N2 from (4-(4-
sulfonatophenylamino) benzene-1-sulfonic acid) _______________________________ 132
Table-A_2.4: The Cartesian coordinates for all the stationary points for the fragmentation of 4-
amino-3(phenyldiazenyl)benzenesulfonte calculated at B3LYP/6-31+G(d) level as illustrated
in Figure-2.17. __________________________________________________________ 133
Table-A_2.5: The Cartesian coordinates for all the stationary points for the fragmentation of (4-
(4-sulfonatophenylamino) benzene-1-sulfonic acid) calculated at B3LYP/6-31+G(d) level as
illustrated in Figure-2.17. _________________________________________________ 147
Table-A_3.1: The Cartesian coordinates for all the stationary points for the fragmentation of
phenoxide anion calculated at B3LYP/6-31+G(d) level as illustrated in Figure-3.3. ____ 153
vi
LIST OF SCHEMES Scheme-1.1: Payne rearrangement_______________________________________________ 14
Scheme-1.2: Payne rearrangement in an unsymmetrical system________________________ 14
Scheme-1.3: Alternative cyclization to oxetane system _______________________________ 14
Scheme-1.4: Fragmentation mechanism from the two isomeric epoxides _________________ 16
Scheme-1.5: Loss of nitrogen from azodye anions. __________________________________ 18
Scheme-1.6: Fragmentation of phenoxide anions____________________________________ 19
Scheme-1.7: Evidence of benzene-oxide and oxepin structures instead of phenoxide anion.__ 19
Scheme-2.1: Proposed dissociation-recombination reaction mechanism__________________ 33
Scheme-2.2: Proposed intramolecular nucleophilic aromatic substitution reaction. __________ 33
Scheme-2.3: Nucleophilic aromatic substitution reaction in the gas-phase ________________ 34
Scheme-2.4: Fragmentation pathways for major ions in the CID spectrum of the azodye 4-amino-
3-(phenyldiazenyl)naphthalene-1-sulfonate (Fig-2.1(a))___________________________ 36
Scheme-2.5: Azo-hydrazone type fragmentation ____________________________________ 36
Scheme-2.6: Resonance contributing structures of the secondary amine _________________ 45
Scheme-2.7: Substitution nucleophilic mechanism in the monoanions of 4-amino-3-((4-
sulfophenyl)diazenyl)naphthalene-1-sulfonate __________________________________ 49
Scheme-2.8: Aromatic substitution reaction involving tautomeric structure ________________ 55
Scheme-2.9: Resonance contributing structure of the tautomer_________________________ 56
Scheme-2.10: Calculated reaction mechanism-1 for 4-amino-3-(phenyldiazenyl) naphthalene-1-
sulfonate _______________________________________________________________ 58
Scheme-2.11: Calculated reaction mechanism-2 for 4-amino-3-(phenyldiazenyl) naphthalene-1-
sulfonate _______________________________________________________________ 59
Scheme-2.12: Calculated reaction mechanism-1 for 4-hydroxy-3(phenyldiazenyl) naphthalene-1-
sulfonate _______________________________________________________________ 64
Scheme-2.13: Calculated reaction mechanism-2 for 4-hydroxy-3(phenyldiazenyl) naphthalene-1-
sulfonate _______________________________________________________________ 65
Scheme-2.14: Preliminary calculation on the dianion system ___________________________ 69
vii
Scheme-3.1: Binkley and coworker’s mechanism of phenoxide fragmentation _____________ 81
Scheme-3.2: Smiles rearrangement in the Gas-Phase________________________________ 81
Scheme-3.3: Fragmentation of phenoxy ethoxide anion_______________________________ 82
Scheme-3.4: Fragmentation of the labeled phenoxy ethoxide anion (Ph16O(CH2)218O-) ______ 83
Scheme-3.5: Fragmentation of the 13C labeled phenoxy ethoxide anion (PhO(CH2)2O-) ______ 84
Scheme-3.6: Fragmentation of Perbenzoate anion___________________________________ 85
Scheme-3.7: Proposed fragmentation pathway for phenoxide decomposition ______________ 86
Scheme-3.8: Resonance contributing structure of the intermediate IM3 __________________ 92
Scheme-3.9: Calculated fragmentation mechanism for phenoxide anion__________________ 93
Scheme-3.10: Calculated pathway of phenoxide fragmentation _________________________ 94
Scheme-3.11: Calculated pathway for oxepin fragmentation ___________________________ 99
Scheme-3.12: Resonance contributing structure of the intermediate IM5 ________________ 100
Scheme-3.13: Resonance structures of methanolate anion ___________________________ 101
Scheme-3.14: Rearrangement of the oxepin to benzene-oxide anion ___________________ 102
Scheme-3.15: Fragmentation pathway for the loss of CHO. ___________________________ 103
Scheme-3.16: Possible rearrangement between ketene and oxepin intermediates _________ 104
Scheme-3.17: Rearrangement of the labeled perbenzoate anion through initial nucleophilic
attack at the ortho position_________________________________________________ 105
Scheme-3.18: Rearrangement of the labeled perbenzoate anion through initial nucleophilic
attack at the ipso position _________________________________________________ 106
viii
ABSTRACT
The tandem mass spectrometer is an ideal tool to probe unimolecular
reactions of ions. Of particular interest are reactions involving skeletal rearrangement of
ions prior to dissociation. Given that such unimolecular reactions occur in the absence of
complicating factors such as solvent and counter ions, within the vacuum environment of
the mass spectrometer, computational methods employing molecular orbital and density
functional theories are ideally suited to examine the reaction mechanisms.
A surprising rearrangement was identified by electrospray ionization
tandem mass spectrometry of anions of azo dyes and the rearrangement was found to
effect a loss of the azo moiety bridging aromatic rings as nitrogen. Even though the
fragmentation reaction was previously reported, we are unaware of any conclusive
mechanistic study. In the present thesis, by combination of tandem mass spectrometry
and computational methods, we have identified that the rearrangement proceeds via an
initial tautomerization, followed by nucleophilic aromatic substitution reaction (Scheme-
1).
NH2
SO3
NN
SO3
NHN
HN
SO3
HN NHN
SO3
NHN N
H
SO3
HN-N2
H
SO3
HN
Scheme-1
For the past two decades, phenoxide anions were reported to undergo
unimolecular fragmentation resulting in the loss of CO. The present thesis presents an
electronic structure calculation study on this unimolecular fragmentation, where in it was
ix
identified that the loss of CO occurs via reaction pathways involving ketene like
intermediates and transition states (Scheme-2).
O CO
CO + CO
H HCO
CO
CO
+ CO
HC
OC
O
C
OCO
H
Scheme-2
x
ACKNOWLEDGEMENT 1. I would like to thank my supervisor Dr Stephen Blanksby, not only for his guidance
and supervision, but also for supporting me through my tough times of my University life.
2. I would also like to thank all the lab members for their support through my degree.
3. Finally, I would like to thank my Mom and Dad for support, guidance and
encouragement in times of uncertainty.
1
CHAPTER ONE: INTRODUCTION
Mass spectrometry is the branch of science which deals with the study of
gaseous ions, with or without fragmentation, which are characterised by their mass to
charge ratio (m/z) and their relative abundances. The technique evolved from the
discovery of positively charged rays by Goldstein in 1886, which was followed by Wein
(1898) studying their electric and magnetic properties.1 In the early 1900’s J. J Thompson
built his parabola mass spectrograph to measure the charge to mass ratio (z/m) for several
ionic species.2 This was followed by Aston’s work, to build instruments to obtain
accurate measurements of the ratios of the stable isotopes of many known elements.3 The
first commercial mass spectrometer dedicated to elucidate organic structure in the
petroleum industry was built in 1934.4 From these beginnings, mass spectrometers were
used for mass separation and to elucidate organic structures.
All mass spectrometers consist of three basic components, namely, the ion
source, the mass analyser and the ion detector (Fig-1.1). The role of the ion source is to
vaporize the analyte in the vacuum environment of the mass spectrometer, and to convert
it into an ionised form. After ions are formed in the source, they are accelerated into the
mass analyser where they are separated in vacuum according to their mass to charge ratio
through the use of electric and/or magnetic fields. Finally, the ions are passed into an ion
detector where the ions are destroyed in a process generating electric current that is
amplified and recorded. Correlation of the position of the mass-analyser and the detection
of ion current yields the mass spectrum.5
2
Fig-1.1: Components of a basic mass spectrometer
Although sample is consumed destructively, the technique is very
sensitive and only trace amount of materials are needed in the analysis. The emergence of
the tandem mass spectrometer offered chemists an opportunity to observe and study the
unimolecular fragmentations of a mass-selected ion. Such studies are of fundamental
importance to understanding the intrinsic reactivity of ions in the absence of solvent and
furthermore provide a characteristic “fingerprint” for structure elucidation in analytical
applications.
1.1 Ionization techniques
The traditional method of ion production in mass spectrometry is electron
ionization (EI) in which the gaseous sample molecules are bombarded with a fast (70 eV)
beam of electrons. Chemical ionization (CI) mass spectrometry, since its introduction by
Munson and Field, has also become a widely used technique.6 CI is related to EI except
that ionization of a reagent gas occurs first rather than direct ionization of the sample
molecule. This is followed by transfer of charge to the sample by various chemical
processes.6
In a typical CI mass spectrometer, the reagent gas (M) is subjected to
high-energy 70 eV electron impact at high pressures. In this process a radical cation (M+.)
is formed (Eq-1).
M M+ e + 2e(70eV) (1)
3
The most commonly used reagent gas is methane and its electron
bombardment at high pressures forms the methane radical cation (Eq-2). The CH4+. then
reacts rapidly with another molecule of methane to form CH5+ and CH3
. (Eq-3). CH5+ is
an extremely powerful proton donor and will react to protonate most molecular analytes
(A), where A is any organic compound (Eq-4).6
CH4 + e CH4 2e+ (2)
CH4 + CH3 + CH5CH4 (3)
CH5 + A AH + CH4 (4)
Chemical ionization is widely used to produce positive ions, but can also
be used to form negative ions in the gas-phase. However, under negative ion CI
conditions, the reagent gas has three important functions. Firstly, the reagent gas serves to
thermalize the electrons by elastic scattering and dissociative ionization process.
Secondly, the reagent gas should capture the thermal electrons by either electron capture
or dissociative electron capture process. Thirdly, the reagent gas should transfer the
negative charge to the analyte molecule by a variety of chemical reactions such as proton
transfer, H2+. abstraction, charge exchange, or nucleophilic displacement.7
The most popular reagent gas used for negative ion CI is a mixture of
methane and nitrous oxide. The thermal electrons produced by electron bombardment of
a mixture of methane and nitrous oxide are captured by N2O to produce O-. (Eq-5). The
atomic oxygen anion radical reacts with CH4 to form hydroxide ion and methyl radical
(Eq-6).
4
RCOO
RCH3COO
O
CH3
C
O
H3C R
+
++
N2O + e N2 + O (5)
O + CH4 OH + CH3 (6)
Hydroxide, being a strong gas-phase base, abstract protons from a wide
range of compounds such as carboxylic acids, alcohols, thiols, ketones and amino acids.8
The other known method is to capture thermal electrons by using a
mixture of nitrous oxide and a non-reactive buffer gas such as N2. This technique
produces the atomic oxygen radical anion that can ionize carbonyl compounds by
nucleophilic displacement (Eq-7, Eq- 8).9
(7) (8)
The CI methods described here provide access to a range of molecular
ions causing very little fragmentation. Hence CI is popular as a technique to gain
molecular mass information.10
After the introduction of electrospray ionization (ESI) by Fenn and co-
workers, ESI has become another popularly used soft ionization method. The method
ionizes samples at atmospheric pressure and has proven to be the best method to
accomplish ionization of bio-molecules as it allows for large, non-volatile molecules to
be analysed directly from the liquid phase.11 This is not possible in a CI source, because
the analytes must be first vapourised, which could cause decomposition of bio-molecules.
In ESI-MS (Fig-1.2), the analyte solution is pumped at a very low flow
rate through a steel capillary, which is maintained at a very high positive or negative
5
voltage, typically 3-5 kV. The resulting field at the tip of the capillary charges the surface
of the emerging liquid. As a result, the liquid protrudes from the capillary tip forming
what is known as a ‘Taylor cone’ (Fig-1.2).12, 13 Droplets from the Taylor cone detach
from the surface when the Coulombic repulsion of the surface is equal to the surface
tension of the solution.14 Molecular ions are formed from these droplets by one of the two
proposed mechanisms, namely, (a) the Coulomb fission mechanism or (b) the ion
evaporation mechanism. The Coulomb fission mechanism assumes that increased charge
density due to solvent evaporation causes large droplets to divide into smaller and smaller
droplets until eventually only charged molecules remain. By contrast, the ion evaporation
mechanism, assumes that the increased charge density that results from solvent
evaporation eventually causes Coulombic repulsion to overcome the droplet surface
tension, resulting in a release of ions directly from the droplet surfaces.12 Regardless of
the formation mechanisms, ESI generates vapour phase ions that can be analysed
according to mass to charge ratio (m/z).
Fig-1.2: Schematic of the electrospray ionization process.12
6
There are four major mechanisms by which the analytes becomes charged
and get discharged as ions during ESI. Such charging can occur either in solution or in
the gas-phase (Taylor cone). They are: (a) ionization in solution, (b) ionization in the gas-
phase, (c) ionization through electro-chemical oxidation and reduction, and (d)
ionization/interaction in solution and gas-phase.12 (a) Ionization in solution is the primary
method by which analytes are ionized during ESI. In general, analytes are ionized in
solution by addition of a base or an acid. Organic and biomolecules possessing basic
sites are protonated in solution by addition of an acid to form their respective [M+H]+
ions, while analytes with acidic moieties are deprotonated by addition of a base to form
their respective [M-H]- ions . The analytes that already exist as ions in solution separate
from counter ions during the formation of Taylor cone and are eventually transferred to
the gas phase by charge separation and/or ion evaporation mechanism.12 (b) ESI is known
to produce, large quantities of charged solvent/analytes in the gas-phase. Sometimes,
analytes uncharged in solution can undergo gas-phase interaction, such as a simple proton
transfer with the charged solvent molecules during the formation of Taylor-cone. In this
way, analytes that evaporate from the droplet as neutrals can become charged through
gas-phase interactions and eventually form ions by charge separation and/or ion
evaporation mechanism.12 (c) Electro-chemical reactions can convert an uncharged
analyte into a charged form by achieving charge balance via an oxidation reaction in the
capillary, in positive ion mode, and reduction reaction in negative ion mode. The analyte
best suited, is one that is easily oxidized or reduced, to form a solution stable ionic
species in the capillary. The stable ions formed, would then be transferred to the gas-
phase by charge separation or/and ion evaporation mechanism.12 One such example of
7
analyte that is known to ionize efficiently by electro-chemical ionization in the ESI
source are the ferrocene derivatives of a variety of alcohols. They were found to form the
corresponding ferrocinium cation of the various alcohols in the gas-phase.15 Polar
analytes that do not contain acidic or basic groups can be charged by preliminary
interaction in solution followed by ionization in the gas-phase by charge separation
or/and ion evaporation mechanism. One such example is the formations of stable ions by
adduct formation. Cole and Zhu have shown that the chlorinated adduct of aniline is
formed when chlorinated solvents such as chloroform are used in the ESI process. This
method allows for successful negative ion ESI detection of molecules that lack an acidic
site.16 Similarly, addition of sodium, lithium, ammonium and potassium salts to samples
with weakly basic or polar, neutral samples aid in the formation of positive ions by cation
attachment in the ESI process.12, 17
1.2 Tandem mass spectrometers
The soft ionization techniques such as chemical ionization and
electrospray ionization generally produce molecular species with low internal energy and
hence show little or no fragmentation. An effort to increase the fragment ion information,
to better characterize the structure of analytes, saw the introduction and the use of the
tandem mass spectrometer. The tandem mass spectrometer is similar to a normal mass
spectrometer, except that it has two mass analysers, with a dissociation region in-between
(Fig-1.3). The dissociation region, is the region where ions may be excited energetically
using a number of different methods namely: (a) Collision Induced Dissociation or (CID),
in which the ions are excited by collisions with neutral atoms or molecule, (b) Photon
Induced Dissociation or (PID), in which the ions are activated by absorption of photons,
8
(c) Surface Induced Dissociation or (SID), in which the ions are excited by collisions
with solid or viscous liquid, and (d) Electron Capture Dissociation or (ECD), in which the
ions are fragmented by dissociative recombination with thermal electrons.18, 19 Each of
these methods leads to the production of charged and neutral fragments through bond
cleavage in the molecular ions.
In analytical applications, the tandem mass spectrometer may be used to
selectively detect an analyte of interest from complex mixtures. The first mass analyser,
transmits only ions of a particular m/z ratio into the dissociation region, where the
fragmentation of ions occur. The second mass analyser is scanned to pass, in turn, the
products of dissociation along with the molecular ion onto the detector. This technique is
routinely used to selectively detect and identify analytes of interest from complex
mixtures by simultaneous identification of fragment ions together with the molecular ion.
Since two mass analysis steps are involved, tandem mass spectrometry is often referred to
as MS/MS or MS2 (Fig-1.3).
Fig-1.3: Components of a tandem in space mass spectrometer (Redrawn from ref)20
The most common method of adding energy to the ions is by collisional
activation. In this process, the mass selected ion collides with a neutral atom or molecule,
in a dissociation region. The overall process occurs in two steps. The first step is very fast
and corresponds to the collision between the precursors ions (mp+) and the target gas (n)
bringing the ions into the excited state (mp+*) (Eq-9). The second step is the unimolecular
9
decomposition of the activated ions to form charged (mf+) and the neutral (mn) fragments
(Eq-10). 19, 21
mp+ + N → mp
+* (9) mp
+* → mf
+ + mn (10)
The choice of the collision gas is important in order to prevent the
reactions of ions with the target gas and also to prevent significant deflections from their
trajectories. For these reasons, He, Ar or N2 are typically used as the collision gas.21
Tandem mass spectrometry was originally developed using electric and
magnetic sector mass spectrometers and was later expanded to include arrangements of
mass/energy analysers, such as multiple quadrupoles22, sectors20, and time-of flight.23
These are called tandem-in-space mass spectrometers (Fig-1.3) since primary and
secondary mass analyses are performed by two analysers that are coupled in series.21
The concept was further extended to tandem-in-time mass spectrometers.
One such example of tandem-in-time mass spectrometer is an ion-trap mass spectrometer.
An ion trap is a quadrupole mass analyser, and can be conceptually thought of a closed
loop of radiofrequency that helps in the storage of ions. The quadrupole mass analyser
can be 3-dimensional or 2-dimensional (linear) in space (Fig-1.4). The mass analyser is
often filled with buffer gas such as helium at an appropriate pressure to reduce the loss of
ions by ion repulsions.5, 24
10
Fig-1.4: Cross section of a linear ion trap
Four major processes occur within the mass analyser that contributes to
performing a successful tandem mass spectrometry experiment with an ion-trap. These
are (i) storage of ions, (ii) isolation of ion of interest: ions of interest can be isolated
according to their mass to charge (m/z) ratio, by expelling all other ions by applying a
destabilizing radio frequency, (iii) collision-induced dissociation (CID) of mass selected
ions: energy can be imparted to the mass-selected ions by collisions with the helium
buffer gas to form fragment ions, and (iv) detection of precursor and fragment ions.24
Additionally, the analyzer can also isolate a particular fragment ion arising
from the dissociation of the precursor ion. The mass-selected ions can be further activated
to undergo fragmentations. These types of experiments are popularly known as MSn
experiments where n represents the number of mass selection and dissociation
experiments. These experiments further help in characterization of the structure of the
fragment ions.24
11
1.3 Elucidation of gas phase fragmentation mechanisms by mass spectrometry and computational study
The soft ionization techniques such as chemical ionization and
electrospray ionization generally produce molecular species with an even number of
electrons, most often by addition or abstraction of a proton, thus producing positive or
negative ions in the gas-phase. Most often, fragmentation of ions involve simple
heterolytic bond cleavages leading to the formation of a stable fragment ion and a neutral.
For example, heterolytic cleavages of a single bond can occur in a
molecular cation forming a smaller cation and displacing a stable neutral (Eq-11). The
initiation of the cleavage depends on the ability of the heteroatom Y to attract the electron
pair. In general, halogens cleave more readily followed by oxygen, sulphur, nitrogen and
carbon. With reference to neutral formation, stability of neutral formed depends on the
ease with which it can leave.25, 26
R YH R + YH (11)
In some instances, cleavages through cyclization displacement are
common in the positive ions. Such cleavages require stabilization of the charge by distant
groups in the same ion and the cleavage occurs via a nucleophilic substitution type
mechanism.25, 26 For example, in Equation-12 the oxygen atom, displaces the cyclic
amino group by a nucleophilic substitution type mechanism forming a stable six member
cyclic ion and a stable six member unsaturated amine.25
(12)
CHN
ON
HN
O+
N
12
The fragmentation of even electron negative ions also follows a number
of predictable rules. In negative ions, simple heterolytic cleavage leading to the
formation of an anion-neutral complex is thought to be an important mechanistic step.
The anion-neutral complex may dissociate directly or undergo ion-molecule chemistry
prior to dissociation.27 For example, collisional activation of the acetate anion leads to
the formation of methyl anion via loss of carbon dioxide. The fragmentation
mechanism would involve a simple heterolytic initial formation of anion-neutral
complex between the methyl anion and carbon dioxide. The anion-neutral complex
then dissociates to form methyl anion via a loss of CO2 ( Eq-13).28
(13)
With reference to the ion-molecule chemistry within the anion-neutral
complex, the anion part of the complex can also undergo proton transfer or nucleophilic
substitution reaction with the neutral, to form a new anion-neutral complex, which would
be followed by dissociation.27 Proton transfer reactions within the anion-complex are
widely observed. For example, collisional activation of the ethoxide anion leads to the
formation of acetaldehyde enolate anion via the loss of H2. The loss of H2 from the
ethoxide anion, would involve the formation of an ion-neutral complex between hydride
ion and acetaldehyde. The hydride ion, then deprotonates the neutral portion to form the
second anion-neutral complex between acetaldehyde enolate anion and H2. The resulting
anion-neutral complex undergoes direct dissociation, driven by the negative charge to
form the enolate anion and H2 neutral (Eq-14).29
H3C CO2 CH3 CO2 CH3 + CO2
13
(14)
In some instances, nucleophilic substitution chemistry can also occur
within the anion-neutral complex. For example, collisional activation of N-ethyl
ethanamide, results in the formation of NCO-, via loss of propane. The loss of propane
from the N-ethyl ethanamide, would involve the initial formation of ion-neutral complex
between methyl anion and ethyl isocyanate. The methyl anion then acts as a nucleophile,
displacing NCO- from the ion-neutral complex, resulting in the production of propane
and the isocyanate anion (Eq-15).27
(15)
In some instances, where simple cleavage is energetically unfavourable,
the ion undergoes skeletal rearrangement prior to fragmentation. The skeletal
rearrangement sometimes shares similar mechanistic character to some of the named
rearrangements that would occur in the condensed phase for the same ion. The course of
the reaction in the condensed phase however often depends on the nature of the solvent
and the counter ions. Such factors, could directly affect the nature of the reacting species.
Whereas in the gas-phase phase, the reaction occurs in the absence of the solvent and
counter ion effects thus providing insight into the intrinsic reactivity of ions.30
Characterization of molecular rearrangements most often requires a
combination of mass spectrometric and computational techniques. One such example is
H H2 H2C C H2 + H2C CH
OH3C CH O
HH
OH2C
H
CHO
H3C CO
N CH2CH3 CH3 C N CH2CH3 C N + C3H8OO
14
the study of Payne rearrangement in the gas-phase by Bowie and co-workers.31 The
Payne rearrangement in the condensed phase involves an intramolecular cyclisation of
the alkoxide anion at the carbon of an epoxide ring to open the epoxy ring and form a
new epoxide ring (Scheme-1.1).32
OO
OO
Scheme-1.1: Payne rearrangement
In the condensed phase, the rearrangement is known to be affected by
three important features: (a) In an unsymmetrical system, such as methyl substituted 2,3
epoxy propoxide anion, the predominant product is normally that which has the more
substituted epoxide (Scheme-1.2).33, 34
OO
OO
A B
Scheme-1.2: Payne rearrangement in an unsymmetrical system
(b) The reaction takes place under the influence of the base, a protic solvent with a high
dielectric constant. (c) In the condensed phase, there is no indication of alternative
cyclisation to form a four membered oxetane system (Scheme-1.3).33, 34
OO
OO
O
O
A B
C
Scheme-1.3: Alternative cyclization to oxetane system
15
In order to verify the occurrence of the Payne rearrangement in the gas-
phase, the Payne rearrangement product of the 2,3-epoxy propoxide anion was
synthesized and was subjected to CID. The MS/MS spectrum of the synthesized Payne
rearrangement product matched with that of dimethyl substituted 2,3-epoxy propoxide
anion (Fig-1.5), thus validating the occurrence of the Payne rearrangement.31
Fig-1.5: The MS/MS spectrum of the 3-methyl- 2,3 epoxybutoxide anion 31 To further investigate the possibility of occurrence of the competing
mechanism (Scheme-1.3), the oxetane intermediate was synthesized independently and
was subjected to Collision-Induced Dissociation. The spectrum obtained matched with
that of the 3-methyl-2,3-epoxybutoxide anion within the experimental uncertainty (Fig-
1.6).31
16
Fig-1.6: MS/MS spectrum of the 2,2-dimethyloxetan-3-olate 31
The result suggests that the Payne rearrangement occurs in the gas-phase.
Moreover the competing oxetane mechanism also occurs in the gas-phase, with the three
structures A, B, C (Scheme-1.3) equilibrating in the gas-phase. 31
From the data it was suggested that the fragment ions at m/z 71 and m/z 43
(Fig-1.5) correspond to the fragment ions from the two epoxides. (Scheme-1.4) Since the
ion at m/z 71 corresponding to the loss of CH2O is the base peak (Fig-1.5), it was
concluded that the more substituted epoxide is the predominant product from the Payne
rearrangement. 31
OO
O
H+ CH2O
m/z 71
OO CH2CHO + CH3COCH3
m/z 43
Scheme-1.4: Fragmentation mechanism from the two isomeric epoxides31
To add to the experimental work, a computational study was conducted to
better understand the energetics of the Payne rearrangement. Figure-1.7 illustrates the
reaction coordinate diagram for the rearrangement with respect to the methyl substituted
17
2,3 epoxy propoxide anion. In the calculated mechanism, the Payne rearrangement of the
epoxide anion (A) to its isomer (B) occurs over a barrier of 33 kJ mol-1. The result clearly
suggests that the barrier to Payne rearrangement is low and is easily accessible.
Surprisingly, the isomeric propoxide B is 14 kJ mol-1 lower than the parent proponoxide
anion. The result suggests that the structure B is more energetically favourable than the
more substituted isomer A. This contradicts the experimental data and the solution phase
observation but is not significant overall as these are not in equilibrium condition.31
Furthermore the calculations suggest that the rearrangement to oxetane intermediate is
feasible from both the two isomeric epoxides A and B. However, the rearrangement to
the oxetane intermediate requires three-fold more energy (117 kJ mol-1 from A) than that
required for the Payne rearrangement.31
O0
-14
O
O
O
O
33
O
O O
O
O
A
B
CC
-43-43
O
O117
O
O
117
TS1
TS2TS3
Fig-1.7: Reaction coordinate diagram of the Payne rearrangement. All energies are in kJ mol-1. 31
18
1.4 Identification of two unusual anion rearrangement in the gas- phase
In this thesis, we have identified two unusual anion rearrangements in the gas-phase, one with the azodye anions and other with the phenoxide anions. (i) In anions of azodyes an unusual fragment ion corresponding to the loss of 28 Da
was observed. Both Richardson and co-workersa and Gaskall and co-workersb in their
studies of the anions of azodyes have also reported the loss of 28 Da. The loss was
proposed to be the loss of N2 from the azodyes but neither group has proposed a
mechanism to account for this observation. What is so interesting about this
fragmentation is that the azo moiety bridging the two aromatic rings is lost as nitrogen,
leaving the two aromatic rings intact (Scheme-1.5). By a combination of previously
described mass spectrometric technique together with complementary computational
study we elucidate the reaction mechanism for this unusual fragmentation
SO3
NH2
NN
CID
-N2
m/z 326
m/z 298
Scheme-1.5: Loss of nitrogen from azodye anions. (ii) In fragmentations of the anions of phenoxide, product ions consistent with the
loss of CO were observed. Even though mass spectrometric study was conducted by both
a Richardson, S. D.; McGuire, J. M.; Thructon, A. D.; Baughman, G. L., Org. Mass Spectrom. 1992, 27, 289. b Sullivan, A. G.; Gaskell, S. J., Rapid Commun. Mass Spectrom. 1997, 11, 803
19
Binkley and co-workersc and Bowie and co-workersd to elucidate the reaction mechanism
(Scheme-1.6), we are unaware of any complementary computational study.
OC
O CO
+ CO
A B C D
Scheme-1.6: Fragmentation of phenoxide anions
Furthermore, in a recent study by Blanksby and co-workers e on the
dissociation of perbenzoate anions fragment ions corresponding to the formation of
phenoxide anion were observed following the loss of CO2. Somewhat surprisingly,
computational studies support the formation of benzene-oxide and oxepin structure as
product ions, instead of the phenoxide anion (Scheme-1.7).The result might suggest that
the benzene-oxide and oxepin intermediates may be linked via facile rearrangement to
phenoxide anion in the gas-phase. In this thesis we would elucidate the possible
rearrangement mechanism of benzene-oxide and oxepin structure to phenoxide by
computational techniques.
OOO
ortho
ipso
OO
O OO
O OCO2
OO
OOOO OC
O
O
CO2O
Scheme-1.7: Evidence of benzene-oxide and oxepin structures instead of phenoxide anion. c Binkley, R. W.; Fletcher, T. W.; Winnik, W., J. Org. Chem. 1992, 57, 5507 d Eichinger, P. C. H.; Bowie, J. H.; Hayes, R. N., J. Am. Chem. Soc. 1989, 111, 4224 e Harman, D. G.; Ramachandran, A.; Gracanin, M.; Blanksby, S. J., J. Org. Chem. 2006, 71, 7996
20
1.5 Computational methods
Computational methods as such have evolved as a complementary
technique for probing the mechanisms of ionic fragmentations and rearrangements in the
gas-phase. Given that reactions are observed in the vacuum environment of the mass
spectrometer, the experimental setup is quite close to a truly isolated system, which is the
primary requirement of molecular orbital or density functional theory calculations. The
combination of mass spectrometry techniques with theoretical calculations allows: (i)
characterization of structures, in which the traditional bonding rules are violated, (ii)
prediction of potentially stable isomers and evaluation of their stability, (iii) formulation
of potential reaction pathways, evaluation of heats of formation of intermediates not
amenable by experimental techniques, (iv) estimation of gas-phase acidity or basicity for
different acids.35
The theoretical models used in the gas phase chemistry are based on ab
initio molecular orbital theory. The ab initio molecular orbital theory is based on the
fundamental laws of quantum mechanics and requires no experimental parameters. The
computations are solely based on the laws of quantum mechanics and on the values of
small number of physical constants such as speed of light, charge and mass of electrons
and nuclei and Planck’s constant. Quantum mechanics states that energy and other related
properties of the molecule may be obtained by solving the Schrödinger equation ( Eq-16).
36, 37
ĤΨ= EΨ (16)
21
Here, Ĥ is the Hamiltonian operator, which when applied to the wave
function Ψ, gives the electronic energy E of the wave function. The ab initio methods,
compute solutions to the equation using a series of rigorous mathematical approximations.
The two most important approximations used by ab initio methods to solve the
Schrödinger equation are the basis set and the theoretical model.36, 37
1.5.1 Basis set
The basis set is a mathematical representation of the molecular orbitals
within the molecule. The basis set can be interpreted as restricting each electron to a
particular region of space.36 GAUSSIAN 0338
offers a number of pre-defined basis sets,
which approximate the molecular electronic wave function, using a linear combination of
atomic orbitals. The basis set assigns a group of basis functions to each atom within the
molecule to approximate its orbitals. The number and types of basis functions that they
contain classify basis sets. These basis functions themselves are composed of a linear
combination of Gaussian functions. Such basis functions are called contracted function
and the component Gaussian functions are referred to as primitives.36 Minimal basis set
such as STO-3G use fixed-size atomic-type orbitals and approximate all orbitals to be of
the same shape.39,40 However, such approximations are often not adequate. There are
several types of extended basis sets, namely split valence basis set, polarized basis set and
diffuse functions, which consider the higher orbitals of the molecule and accounts for size
and shape of molecular charge distributions.
The split valence basis sets, increases the size of the orbital generated, by
increasing the number of basis functions per atom.36 An example of split valence basis set
is 6-31G, which uses two sizes of basis function for each valence orbital. It uses one
22
Gaussian type function for inner shell and for its outer shell uses two basis functions, one
is a linear combination of three primitives and other is a diffuse primitive.36, 41 Similarly,
triple split valence basis sets, such as 6-311G, use three sizes of contracted functions for
each valence orbital type.42 Hence, split valence basis sets allow orbitals to change in size,
but not to change shape.
Polarised basis sets remove this limitation by adding orbitals with angular
momentum beyond what is required for the ground state to the description of each
atom.36, 40 Polarised basis sets acknowledge and account for the fact that, when atoms are
brought close to each other, their charge distribution causes polarization effect i.e. the
positive charge is drawn to one side while the negative charge is drawn to the other side,
thus resulting in distorting the shape of the atomic orbitals. This results in the ‘s’ orbital
sharing the characteristics of the ‘p’ orbitals and the ‘p’ orbital to share the characteristics
of the ‘d’ orbitals. Hence the use of a polarised basis set results in a better approximation
than a split valence basis set alone, which treated atomic orbitals as existing only as
‘s’, ’p’, ’d’ etc.40 Polarised basis sets are represented by (d) or (p), e.g. 6-31G(d) and 6-
31G(d,p). In 6-31G(d) basis set, d functions are added to the heavy atoms, whereas in 6-
31G(d,p), p functions are added to the s orbitals of hydrogen atoms in addition to d
functions on heavy atoms.36, 40
Diffuse functions are large-size versions of s and p type function and
hence allow the molecular orbital to occupy a larger region in space.36, 43 The diffuse
functions are important for systems where electrons are relatively far away from the
nucleus, e.g., molecules with lone pair of electrons, anions and other systems with
significant negative charge, systems in their excited states, systems with low ionization
23
potentials, and description of absolute acidities. Diffuse functions are designated with a
‘+’ e.g. 6- 31+G(d), 6-31++G(d,p). In 6-31+G(d), diffuse functions are added to the
heavy atoms whereas in 6-31++G(d,p), diffuse functions are added to the hydrogen atoms
as well.36, 43
1.5.2 Theoretical model
A hybrid method, ‘Becke’s three-parameter non-local potential’ or
otherwise known as B3LYP was employed in the study.44 The hybrid method uses a
combination of Hartree-Fock (HF) and Density Functional Theory (DFT) theories.36, 44 In
the HF method, wave function Ψ0 is written as a product of one electron wave function or
spin orbitals (Eq-17). The spin orbitals Ψi are expanded as a linear combination of basis
functions (Φ).
Ψi=Σ Ci uΦu (17) HF solves the wave function assuming that each electron is moving in an
average electron distribution produced by other electrons. But it does not take into
account the electron correlation effect, i.e., how electrons in a molecular system respond
to each others motion. It is also inefficient for accurate modelling of energetics of
reaction and bond dissociation energies, which is essential for examining ion dissociation
in this study.36, 45
In recent years, DFT methods have gained popularity, as it takes into
account the electron correlation effect. DFT achieves greater accuracy than HF theory at
a modest increase in computing time.36 DFT theories are based on the fact that the
ground-state electronic energy is completely determined by the electron density (ρ). DFT
methods compute electron correlation via general functionals of the electron density. The
24
approximate functionals used by DFT methods, partition the electronic energy as sum of
three terms, kinetic energy, attraction between nuclei and electron, Coulomb repulsion,
and an exchange-correlation term. The exchange-correlation term accounts for the
remainder of the electron-electron interaction, which itself are divided into separate
exchange and correlation components. The difference between the various DFT methods
lies in the way the exchange and correlation components are treated by the functionals.36,
46 A variety of functionals have been defined such as, local exchange and correlation
functionals and gradient-corrected functionals (non-local). The local exchange and
correlation involve only the values of electron spin densities whereas the gradient-
corrected functionals involve both the electron spin densities and their gradients.36 A
popular gradient-corrected exchange functional is one proposed by Becke in 1988.47 A
widely used gradient-corrected correlation functional is the LYP functional of Lee, Yang
and Parr.48 The combination of Becke’s gradient-corrected exchange functional and the
LYP functional forms the B-LYP method.
Several functionals have been defined, which treat exchange functionals as
linear combination of HF, local and gradient-corrected exchange terms. Such functionals
are referred to as the hybrid functionals. The most popular one of this type is B3LYP
method.44 B3LYP method has become increasing popular because of its ability to
generate accurate results with only a modest increase in computing resource.
25
References for chapter one
1. Goldstein, E., Berl. Ber. 1886, 39, 691. 2. Thomson, J. J., Rays of Positive Electricity and Application to Chemical Analyses.
2nd ed.; Longmans, Green & Co.: London, 1922. 3. Aston, F. W., Philosophical Magazine (1798-1977) 1920, 40, 628. 4. Smythe, W. R.; Rumbaugh, L. H.; West, S. S., Phys. Rev. 1934, 45, 724. 5. Downard, K., Mass spectrometry: A foundation course. Royal Society of
Chemistry: Cambridge, 2004. 6. Munson, M. S. B.; Field, F. H., J. Am. Chem. Soc. 1966, 88, (12), 2621. 7. Harrison, A. G., Chemical ionization mass spectrometry. 2nd ed.; CRC Press:
Boca Raton, 1992. 8. Smith, A. L. C.; Field, F. H., J. Am. Chem. Soc. 1977, 99, (20), 6471. 9. Harrison, A. G.; Jennings, K. R., J. Chem. Soc., Faradays, Trans. 1 1976, 72,
1601. 10. Chapman, J. R., Practical Organic Mass Spectrometry: A Guide for Chemical
and Biochemical Analysis. J. Wiley: Chichester; New York, 1993. 11. Mann, M.; Meng, C. K.; Fenn, J. B., Proceeding of the 36th Annual
Conference on Mass Spectrometry and Applied topics 1988, 1207-08. 12. Cech, N. B.; Enke, C. G., Mass Spectrom. Rev. 2001, 20, 362. 13. Fenn, J. B.; Mann, M.; Meng, C. K.; Wong, S. F.; Whitehouse, C. M., Science
1989, 246, (8), 64. 14. Taflin, D. C.; Ward, T. L.; Davies, J. D., Langmuir 1989, 5, 376. 15. Van Berkel, G. J.; Quirke, J. M E.; Tigani, R. A.; Dilley, A. S., Anal. Chem. 1998,
70, 1544. 16. Cole, R. B.; Zhu, J., Rapid Commun. Mass Spectrom. 1999, 13, 607. 17. Saf, R.; Mirtl, C; Hummel, K., Tetrahedron Lett. 1994, 35, 6653.
26
18. Busch, K. L.; Glish, G. L.; McLuckey, S. A., Mass Spectrometry/Mass
Spectrometry: Technques and Applications of Tandem Mass Spectrometry. VCH: NewYork: 1988.
19. Sleno, L.; Volmer, D. A., J. Mass Spectrom. 2004, 39, 1091. 20. McLafferty, F. W.; Todd, P. J.; McGilvery, D. C.; Baldwin, M. A., J. Am. Chem.
Soc. 1979, 102, (10), 3360. 21. Shukla, A. K.; Futrell, J. H., J. Mass Spectrom. 2000, 35, 1069. 22. Yost, Y. A.; Enke, C. G., J. Am. Chem. Soc. 1978, 100, 2274. 23. Glish, G. L.; Goeringer, D. E., Anal. Chem. 1984, 56, 2291. 24. Hoffman, E. De; Stroobant, V., Mass spectrometry: principles and applications.
Chichester; New York: Wiley: 2001. 25. McLafferty, F. W., Org. Mass Spectrom. 1980, 15, (3), 114. 26. McLafferty, F. W., Interpretation of mass spectra. Third Edition ed.; University
Science Books: Mill Valley, California, 1980. 27. Bowie, J. H., Mass Spectrom. Rev. 1990, 9, 349. 28. Budzikiewicz, H.; Poppe, A.; Stockyl, D., Int. J. Mass Spectrom. Ion Processes
1983, 47, 217. 29. Hayes, R. N.; Sheldon, J. C.; Bowie, J. H.; Lewis, J. Chem. Soc. Chem. Commun.
1984, 21, 1431. 30. Eichinger, P. C. H.; Dua, S.; Bowie, J. H., Int. J. Mass Spectrom. Ion Processes
1994, 133, 1. 31. Dua, S.; Bowie, J. H.; Taylor, M. S.; Buntine, M. A., Int. J. Mass Spectom. Ion
Processes 1997, 165/166, 139. 32. Payne, G. B., J. Org. Chem. 1962, 27, 3819. 33. Behrens, C. H.; Ko, S. Y.; Sharpless, B.; Walker, F. J., J. Org. Chem. 1985, 50,
5687. 34. Bonini, C.; Guikiano, C.; Righi, L.; Rossi, L., Tetrahedron Lett. 1992, 7429. 35. Alcami, M.; Mo, O.; Yanez, M., Mass Spectrom. Rev. 2001, 20, (4), 195.
27
36. Foresman, J. B.; Frish, E., Exploring chemistry with electronic structure method. Gaussian, Inc: Pittsburg, PA, 1996.
37. Hehre, W. J. Random, L. Schleyer, P. v. R. Pople, J. A., Ab Initio Molecular
Orbital Theory. Wiley: New York, 1986. 38. Gaussian 03 (Revision C.02). Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.;
Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, Jr., J. A.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; and Pople, J. A.; Gaussian 03, Revision
C.02, Gaussian, Inc.: Wallingford CT, 2004. 39. Hehre, W. J.; Stewart, R. F.; Pople, J. A., J. Chem. Phys. 1969, 51, 2657. 40. Hehre, W. J., Ab Initio Molecular Orbital Theory. Acc. Chem. Res. 1976, 9, 399. 41. Hehre, W. J.; Ditchfied, R.; Pople, J. A., J. Chem. Phys. 1972, 56, 2257. 42. Krishnan, R.; Binkley, J. S.; Seeger, R.; Pople, A. J., J. Chem. Phys. 1980, 72,
650. 43. Frisch, M. J.; Pople, J. A.; Binkley, J. S. J., J. Chem. Phys. 1984, 80, 3265. 44. Becke, A. D., J. Chem. Phys. 1993, 98, 5648. 45. Szabo, A.; Ostlund, N. S., Modern quantum chemistry. McGraw-Hill: New york,
1986. 46. Dreizler, R. M.; Gross, E. K. U., Density functional theory: An approach to the
quantum many-body problem. Springer-Verlag: Berlin; New York, 1990. 47. Becke, A. D., Phys. Rev. A 1988, 38, 3098. 48. Lee, C.; Yang, W.; Parr, R.G., Phys. Rev. B 1988, 37, 785.
28
CHAPTER TWO: EVIDENCE OF AN INTRAMOLECULAR
NUCLEOPHILIC AROMATIC SUBSTITUTION: AN
EXPERIMENTAL AND THEORETICAL STUDY OF THE
GAS-PHASE REARRANGEMENT OF AZO DYES
Abstract
NH2
SO3
NN
SO3
NHN
HN
SO3
HN NHN
SO3
NHN N
H
SO3
HN-N2
H
SO3
HN
SO3
NHN
NH
SO3
HNN2
SO3
NHN
NH
A surprising rearrangement was identified in the gas-phase by electrospray
ionization tandem mass spectrometry of anions of azo dye, and the rearrangement was
found to effect a loss of the azo moiety bridging aromatic rings as nitrogen. The collision-
induced dissociation (CID) of substituted analogues of the azo dyes, provide evidence for
the involvement of a nucleophlic aromatic substitution reaction mechanism in the
rearrangement process. Isotopic labeling of the azo dye anion, reveals the involvement of
the tautomer during the fragmentation process. The participation of tautomerization in
this intramolecular nucleophilic aromatic substitution mechanism was further supported
29
by electronic structure calculations carried out at B3LYP/6-31+G(d) level of theory.
Somewhat surprisingly, however, the computational data indicate that the rate
determining step is not via a Meisenheimer transition state. The novel rearrangement
was also found to occur in dianions of the azo dye, where Coulombic repulsions would be
expected to dominate the fragmentation process in the gas-phase.
30
2.1 Introduction
Azo dyes are characterized by the presence of one or more azo moieties
(−N=N−) bridging aromatic rings. The resulting extended conjugation gives rise to strong
absorption maxima in the visible spectrum and thus a range of desirable colours used in
diverse applications including textile dyes, paint pigments, printing inks, and food
colourings.1 As a result of their extensive use, millions of tones of azo dyes are produced
by dyeing industries around the world. To facilitate the dyeing process, azo dyes are often
modified to include sulfonate moieties that improve their water solubility.1
During the manufacture and use of azo dyes, large quantities of azo dyes,
together with their degraded products are discarded in wastewater and as solid residue.
The effluents from these industries often find their way into the aquatic environments.
Their presence in the aquatic environments, not only bring aesthetic objections but also
create hazardous degradation products, such as aromatic amines that are known
mammalian carcinogens.2 As a result, their analysis and detection in wastewater has
become very important, and led to increasing numbers of published methods.3
The most popular method for detecting the presence of azo dyes in
environmental samples makes use of their ultraviolet-visible (UV-Vis) spectral
properties4 coupled to High Pressure Liquid Chromatography (HPLC) or Thin Layer
Chromatography (TLC) for separation of components from each other and the matrix.4, 5
However, with the introduction of mass spectrometry, dyes have been analyzed by
coupling mass spectrometry with HPLC. The most popular ionization technique that has
been employed in conjunction with mass spectrometric techniques is electrospray
ionization, as the sulphonic acid moieties in the azo dyes are readily ionizable to produce
31
[M-H]- anions.6-8 However, azo dyes have also been analyzed by other ionization
methods namely Field Desorption (FD)5, Plasma Desorption (PD)9, Fast Atom
Bombardment (FAB)10, thermospray11, and Matrix Assisted Laser Desorption Ionization
(MALDI).8 Analysis of azo dyes in waste water has been simplified by using tandem
mass spectrometry. Tandem mass spectrometry or MS/MS offers selective detection of
analytes of interest from complex mixtures and hence the detection of azo dyes from the
waste water requires no purification steps.7, 8 Much of the previous work on detection of
azo dyes from environmental samples using MS/MS has focused on detection of
structurally diagnostic fragment ions arising from the azodye anions. Azo dyes show
characteristic fragments corresponding to the loss of SO3 and SO2 and these fragments
were routinely used to rapidly screen the presence of azo dyes in environmental samples.
11,12,13,14
Richardson and co-workers, in an attempt to obtain further structural
information to better characterize sulfonated azo dyes, have reported fragments
corresponding to the so-called ‘azo cleavage’, i.e., fragments arising from homolytic
bond cleavage from either side of the azo moiety.7 Interestingly, in their study a
characteristic fragment corresponding to the loss of 28 Da was also observed. Gaskell and
co-workers in their study have also noted the loss of 28 Da. The loss was proposed to be
the loss of N2 from the azo dyes but neither group has proposed a mechanism to account
for this surprising observation.7, 12 Bowie in his study with aromatic azo benzenes under
Electron-Ionization (EI) condition also reported this interesting loss of nitrogen. However
the mechanism effecting the reaction in radical cations, under EI conditions is likely to be
different.13 What is so interesting about this fragmentation is that the azo moiety bridging
32
the two aromatic rings is lost as nitrogen, leaving the two aromatic rings intact. This
suggests that new bonds are formed between the remaining two aromatic rings.
In the present study we have generated a range of sulfonated azodye
anions in the gas-phase by electrospray ionization of basic solutions of the azo dyes (Fig-
2.1). These ions were activated by collisions with neutral atoms such as Helium or Argon
to induce unimolecular fragmentation in order to study and elucidate the mechanism for
the loss of nitrogen.
Fig-2.1: Range of azo compounds
In our study, we have proposed two intramolecular mechanisms that could
conceivably account for the loss of N2, one representing a simple dissociation-
recombination reaction and the other representing an intramolecular nucleophilic
aromatic substitution reaction. The dissociation recombination mechanism involves a
simple bond homolysis of the azo moiety (Scheme-2.1), followed by the liberation of
nitrogen and formation of an ion-dipole complex. Bowie in his pioneering work with
fragmentation of negative ions has highlighted the importance of the formation of ion-
dipole complex, prior to dissociation to the fragment ions. The formation of fragment
X
SO3H
NN
Y
(a) X = NH2, Y = H
(b) X = NH2, Y = OMe
(c) X = NH2, Y = NO2
(d) X = NH2, Y = Ph
(e) X = NH2, Y = SO3H
(f) X = OH, Y = H
4-amino-3-(phenyldiazenyl)naphthalene-1-sulfonic acid
4-amino-3-((4-methoxyphenyl)diazenyl)naphthalene-1-sulfonic acid
4-amino-3-((4-nitrophenyl)diazenyl)naphthalene-1-sulfonic acid
4-amino-3-(biphenyl-4-yldiazenyl)naphthalene-1-sulfonic acid
4-amino-3-((4-sulfophenyl)diazenyl)naphthalene-1-sulfonic acid
4-hydroxy-3-(phenyldiazenyl)naphthalene-1-sulfonic acid
33
ions from the ion-neutral complex can be effected by reactions such as proton transfer
and nucleophilic substitution within the complex.14 Here we propose the naphthyl radical
anion and the phenyl radical would undergo recombination within the ion-dipole complex
to form the product.
SO3
NH2
NN
SO3
NH2
N2 recombination
SO3
NH2
Scheme-2.1: Proposed dissociation-recombination reaction mechanism
The nucleophilic aromatic substitution proposal involves the attack of
naphthyl amine on to the benzene ring at the ipso position (Scheme-2.2) to form a
resonance stabilized Meisenheimer intermediate (b). The Meisenheimer intermediate
would then undergo an elimination process to eject nitrogen as a neutral (Scheme-2.2)
leaving a charge separated intermediate (c). The resulting intermediate would then
undergo a facile 1,3-proton transfer to form the amine bridged product (d).
NH2
SO3
N
SO3
H2N
SO3
HN
SO3
N H2N NN
-N2 1,3-H+ Transferipso attack
(c) (d)(a) (b)
Scheme-2.2: Proposed intramolecular nucleophilic aromatic substitution reaction.
The mechanism as written in Scheme-2.2 could be considered as charge
remote reaction. A charge remote reaction is defined as one which is uninfluenced by the
charged centre and occurs remote from the centre. Interestingly, the mechanism in
34
Scheme-2.2 is not driven by the negative charge and indeed occurs remote from it.
However, the Hammett σp value for the SO3- is reported as +0.35 and thus is expected to
influence the nucleophilicity for the para-amine moiety. As a consequence the
mechanism might still be considered as influenced by the charge and thus not charge
remote by definition.f
Riveros has recently demonstrated bimolecular nucleophilic aromatic
substitution in the gas phase, in which the fluoride anions displace the nitro substituent
from the benzene ring to from fluoro-benzene (Scheme-2.3).15 It seems possible that the
azo dyes might present a possible unimolecular example of such a process in the gas-
phase.
NO2
+ F
NO2F F
+ NO2
Scheme-2.3: Nucleophilic aromatic substitution reaction in the gas-phase15
In the present study we elucidate the reaction mechanism for the loss of
nitrogen via (i) comparison of homologues substituted on the benzene ring (Fig-2.1(a-f)),
(ii) change of nucleophile, (iii) deuterium exchange and MS3 experiments and
(iv) quantum chemical calculations
2.2 Results and discussion
2.2.1 Collision induced dissociation (CID) of deprotonated azo dyes
Fig-2.2 shows the negative ion CID mass spectrum of the [M-H]- anions
from 4-amino-3-(phenyldiazenyl)naphthalene-1-sulfonic acid (Fig-2.1(a)). The spectrum
f Adams, J., Mass Spectrom. Rev., 1990, 9, 141.
35
was obtained using an electrospray ionization linear ion-trap mass spectrometer. The [M-
H]- molecular ion is observed at m/z 326.
Fig-2.2: CID Spectrum of the azodye 4-amino-3-(phenyldiazenyl)naphthalene-1-sulfonic acid as shown in Fig-2.1(a)
The prominent fragment ions in the spectrum are observed at m/z 262 (-64
Da) corresponding to the loss of SO2 and at m/z 246 which corresponds to the neutral loss
of SO3 (Scheme-2.4). The driving force for the loss of SO2, is the formation of stable SO2
molecule and a very stable phenoxide anion. Binkley and co-workers have reported such
fragmentation from aromatic sulfonate anions.16 The driving force for the loss of SO3, is
the formation of a stable SO3 molecule and a relatively stable phenide anion.
The product ion at m/z 221 corresponds to the loss of 105 Da resulting
from the concomitant loss of N2 and the phenyl radical and results from the so-called
azo-cleavage (Scheme-2.4).7 The other prominent fragment ion observed at m/z 234 (-92
Da) occurs from either the loss of anilinyl radical or from consecutive losses of SO2 and
220 240 260 280 300 320m/z
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
95
100
Re
lativ
e A
bund
ance
325.9
246.0
233.9
220.9 262.0
297.9
295.9308.9
NH2
SO3-
NN
CID
36
N2. The minor fragment ions at m/z 296 (-30 Da) and m/z 309 (-17 Da) could correspond
to the loss of hydrazine (N2H2) and ammonia (NH3) respectively. The fragment ions that
represent the facile loss of nitrogen, are observed at m/z 298 (-28 Da), with an abundance
of 15% of the molecular ion
SO3
NH2
NN
O
NH2
NN
m/z 262
m/z 326
NH2
NN
m/z 246
SO3
NH2m/z 221
SO3
NH
N
m/z 234
SO3
HN
m/z 298
SO2
SO3N2
NH
+ N2
Scheme-2.4: Fragmentation pathways for major ions in the CID spectrum of the azodye 4-amino-3-(phenyldiazenyl)naphthalene-1-sulfonate (Fig-2.1(a))
The loss of anilinyl radical, resulting in the formation of fragment ion at
m/z 234 is proposed to occur via an initial azo-hydrazone tautomerization followed by the
cleavage of the N-N bond from the hydrazone tautomer (Scheme-2.5). Fragmentation of
this type has been previously reported and rationalized by Gaskill and co-workers.12
SO3-
HN
N
NH
SO3-
NH
N
NH
SO3-
NH
N
NH
Scheme-2.5: Azo-hydrazone type fragmentation
37
The consecutive losses of N2 and SO2 from the parent anion resulting in
the formation of ions at m/z 234 were identified through MS3 experiments. One such
experiment involves the initial selection of the product ion at m/z 262 from the CID
spectrum of the molecular ion. The selected ion at m/z 262 when subjected to CID,
fragments to give the ion at m/z 234 (Fig-2.3). A plausible mechanism for this
fragmentation would involve an initial loss of SO2 from the parent azo anion to give a
phenoxide type intermediate. The intermediate could then undergo the loss of azo moiety
as nitrogen, by analogy to the parent ion.
Fig-2.3: CID mass spectrum of the mass selected product ion at m/z 262
The other experiment involves the mass selection of the product ion at m/z
298, from the CID spectrum of the molecular ion. The selected ion at m/z 298 when
subjected to CID, fragments to give ions at m/z 234 (Fig-2.4). A plausible mechanism for
this process could be the reverse of the previous mechanism, where the loss of SO2
NH2
SO3-
NN
140 160 180 200 220 240 260m/z
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
95
100
Rel
ativ
e A
bund
ance
233.9
183.9
261.9154.8
234.9142.9 232.9
127.9 192.9155.9 231.9168.8
CID
m/z 262
-SO2
CID
38
occurs from the m/z 298 that is formed from the loss of nitrogen from the parent azo
anion.
220 230 240 250 260 270 280 290 300m/z
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
95
100
Rel
ativ
e A
bund
ance
233.9
297.9
Fig-2.4: CID mass spectrum of the mass selected product ion at m/z 298
2.2.2 Solution phase labelling
In an effort to establish the structure of the ions at m/z 309, m/z 296 and
m/z 234, the sample 4-amino-3-(phenyldiazenyl)naphthalene-1-sulfonic acid (Fig-1(a))
was dissolved in a solvent mixture of D2O/acetonitrile (80% v/v). The most exchangeable
hydrogens in the molecule would be those on the amine functional group. The resulting
solution was then analysed by ESI-MS (Fig-2.5). The spectrum shows ions m/z 327, m/z
328 apart from the unlabeled molecular ion at m/z 326. The two ions at m/z 327 and m/z
328 represent one deuterium and two deuteria exchanged molecular ions.
NH2
SO3-
NN
m/z 298
CID -N2
CID
39
318 320 322 324 326 328 330 332 334 336m/z
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
95
100
Rel
ativ
e A
bund
ance
328.4
327.5
329.4
326.5 330.3
Fig-2.5: MS spectrum of deuterium labeled sample
Upon mass selection and CID of the ions at m/z 328, the fragment ion
representing the loss of NH3 in the original spectrum, is shifted by a mass unit of 2 Da
(m/z 309) (Fig-2.6). This indicates that the exchanged deuterium at the amine site of the
molecule is lost as a neutral NHD2. The result hence suggests that the amine moiety is
lost as ammonia, with one extra hydrogen extracted from the ring. However, the fragment
ion representing the loss of N2H2 in the original mass spectrum, showed no mass shift in
labeled ESI MS/MS spectrum (Fig-2.6). This suggests that the loss of N2H2 involves
hydrogens from the aromatic rings. However other isobaric losses such as CH2O or NO
can not be ruled out.
Interestingly, ESI MS/MS of the labeled sample also isolated the product
ion that was proposed to arise from the loss of anilinyl radical, which in the original
40
spectrum was masked with fragment ions from consecutive losses of SO2 and N2. The
ESI-MS/MS spectrum of the m/z 328 ion showed two major product ions at m/z 235 and
m/z 236 (Fig-2.6). The fragment ion at m/z 235 would correspond solely to the loss of
deuterated anilinyl radical (-93 Da), whereas the fragment ion at m/z 236 (-92 Da) would
correspond to ions arising from consecutive losses of N2 and SO2. Surprisingly, the
abundance of the ion at m/z 236 is very small, indicating that the contribution from the
loss of SO2 and N2 is neglible as compared to that from the anilinyl radical loss (Fig-2.6).
The result suggest that the tautomer is actively involved in the fragmentation process of
the 4-amino-3-(phenyldiazenyl)naphthalene-1-sulfonate anion.
Fig-2.6: CID mass spectrum of completely deuterium exchanged sample
220 240 260 280 300 320m/z
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
95
100
Rel
ativ
e A
bund
ance
248.1
328.1
235.0
264.1
223.0
300.1236.1
298.1 309.1234.0
ND2
SO3-
NN
CID
41
2.2.3 Evidence towards the mechanism for N2 loss
2.2.3.1 Positive ion experiment
In order to form positive ions of the azodye 4-amino-3-
(phenyldiazenyl)naphthalene-1-sulfonic acid was dissolved in aqueous acetonitrile (50%
v/v) solution containing approximately 2% formic acid solution, before subjecting them
to electrospray ionization. ESI MS/MS spectrum of the [M+H]+ ions of the 4-amino-3-
(phenyldiazenyl)naphthalene-1-sulfonic acid (Fig-2.1(a)) is shown in Fig-2.7. The
[M+H]+ molecular ion is observed at m/z 328.
Fig-2.7: CID mass spectrum of the positive ions of the azodye 4-amino-3-(phenyldiazenyl)naphthalene-1-sulfonic acid as in (Fig-2.1(a))
The prominent fragment ions in the spectrum are observed at m/z 312 (-16
Da) corresponding to the loss of NH2 or O and at m/z 247 which corresponds to the loss
of HSO3. The fragment ion corresponding to the loss of N2 and phenyl radical i.e from
140 160 180 200 220 240 260 280 300 320m/z
0
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
246.9 327.9
247.9
311.9
310.9
221.8217.9
141.8 248.9230.9157.8 169.8 216.9 263.9
298.9
287.9189.8
x50
NH3
SO3H
NN
CID
42
the so-called azo cleavage is also observed at m/z 222. The fragment ions corresponding
to the loss of SO3 and OH were observed at m/z 248 and m/z 311.
Interestingly, the spectrum shows only a small fragment ion abundance at
m/z 299 corresponding to the loss of nitrogen. In Fig-2.7 it has been amplified 50 times
its original abundance. This result is in contrast to the Bowie’s observation with
positively charged radical ion, where the loss of nitrogen was more prevalent.13 In most
instances, reactions of radical ions differ from that of the closed-shell ions and hence
such a result is rather not surprising.
In regards to our proposal, in the positive ion mode, we would expect the
nucleophilic aromatic substitution mechanism to be switched off as the ammonium ion, is
too poor a nucleophile to effect nucleophilic substitution. Hence, the result suggests that
the dissociation-recombination mechanism might be occurring but only in a minor extent.
2.2.3.2 Dianion Experiment
The azo dye 4-amino-3-((4-sulfophenyl)diazenyl)naphthalene-1-sulfonic
acid (Fig-2.1(e)) would be expected to form dianions in the gas-phase, since it has two
ionizable sulphonic acid moieties. ESI-MS/MS spectrum of the [M-2H]2- ions of the
azodye was obtained and is presented in (Fig-2.8). The [M-2H]2- ions is observed at m/z
202.5 in the spectrum.
43
60 80 100 120 140 160 180 200 220 240 260 280m/z
0
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
95
100
Rel
ativ
e A
bund
ance
171.0
234.0
202.5152.0 188.5 221.0156.0
79.9 172.0
Fig-2.8: CID mass spectrum of [M-2H]2- ions from the azo dye 4-amino-3-((4sulfophenyl)diazenyl) naphthalene-1-sulfonic acid as in Fig-2.1(e)
The CID mass spectrum shows a pair of fragment ions at m/z 221 and m/z
156, resulting from the loss of N2 via the azo cleavage. The product ion at m/z 221
corresponds to the sulphonated naphthyl radical anion, while the ion at m/z 156
corresponds to the sulphonated phenyl radical anion. The CID mass spectrum also shows
a pair of fragment ions at m/z 234 and m/z 171, resulting from the cleavage of the N-N
bond from the hydrazone tautomer via an intial azo-hydrazone tautomerization. The
product ion at m/z 234 corresponds to the sulphonated diimino radical anion while the
product ion at m/z 171 corresponds to the sulphonated anilinyl radical anion. The
fragment ion at m/z 188.5 corresponds to the loss of 14 Da. Since the fragment ion
formed after the loss of N2 would also be doubly charged, the product ion at m/z 188.5
corresponds to the loss of N2.
NH2
SO3
NN
SO3
CID
44
The presence of the fragment ion at m/z 188.5 is surprising as it suggests a
rearrangement of a dianion, prior to fragmentation. The result also suggests that the loss
of nitrogen is unlikely to occur via the proposed dissociation-recombination mechanism
(Scheme-2.1). This is because, the initial homolytic cleavage of the parent ion, would
result in the formation of two anions from either side of the azo moiety. The resulting
anions would experience Coulombic repulsion and would not exist as the stable complex
(Scheme-2.1). Hence, the dianion experiment suggests that dissociation-recombination
reaction is unlikely to effect the facile loss of azo moiety as nitrogen.
2.2.3.3 Authentic product experiment
In order to verify the likelihood of nucleophilic aromatic substitution
reaction effecting the loss of N2, secondary amine product (Scheme-2.2(d)) from the
aromatic substitution reaction proposal was synthesized and was then subjected to
tandem mass spectrometric analysis (MS/MS). Figure-9 shows the comparison of the
MS/MS spectrum (Fig-2.9(a)) of the proposed amine product with that of the
MS/MS/MS spectrum (Fig-2.9(b)) from the negative ion of 4-amino-3-
(phenyldiazenyl)naphthalene-1-sulfonic acid (Fig(2.1(a)). It can be seen that both the
spectra have the same fragment ions at m/z 234 and m/z 218, corresponding to the loss of
SO2 and SO3 respectively. The abundance of the fragment ions compared with the
molecular ion, however are noticeably different, even with the same collisional
conditions. This could be, due to either (a) the presence of various positional isomers in
the sample of the synthesized amine. The authentic amine was synthesized by
sulphonating the secondary amine precursor in the presence of sulphuric acid. The
resonance contributing structures of the amine (Scheme-2.6), dictate the course of the
45
reaction and thus sulphonation can occur at a number of positions. The para positions
(Scheme-2.6(a, h)) are generally favoured over the others and thus the resulting mixture
that was analysed would have consisted of large proportions of the two para positional
isomers (Scheme-2,6(c), Scheme-2.6(h)).
NH NH NH NH
NHNHNHNH
(a) (b) (c) (d)
(e)(f)(g)(h)
Scheme-2.6: Resonance contributing structures of the secondary amine
(b) The differing ion abundances could also be due to the difference in internal energy of
the molecules in the two samples, as different energies could be imparted during
successive collisional experiments.
46
220 240 260 280 300m/z
10
20
30
40
50
60
70
80
90
100
10
20
30
40
50
60
70
80
90
100R
elat
ive
Abu
ndan
ce
234.1298.1
218.1234.1
298.0
218.1
MS/MS
MS/MS/MS
Fig-2.9: Comparision of MS/MS spectra of the secondary amine product with that of the MS3 spectrum of the azo dye anion, 4-amino-3-(phenyldiazenyl)naphthalene-1-sulfonate (Fig-1(a))
In general, complete sulphonation of aromatic compounds leads to
additions of sulfonate groups at multiple positions on the aromatic ring. In this case, the
favoured product after complete sulphonation would be a disubstituted product (4-(4-
sulfonatophenylamino)naphthalene-1-sulfonic acid) with substitution at the para position
of both rings. Hence dianions of this compound would be the product from the
nucleophilic aromatic substitution proposal (Scheme-2.2) for the azodye 4-amino-3-
((4sulfophenyl)diazenyl) naphthalene-1-sulfonic acid (Fig-2.1(e)) .
To overcome the ambiguity in the monosulfonated case, a similar
experiment was conducted by obtaining MS/MS spectrum of the corresponding
disulfonated amine product. Figure-2.10, shows the comparision between the MS/MS
NH2
SO3
NN
HN
SO3
CID (a)
CID
m/z 298
CID (b)
47
spectrum of the amine (Fig-2.10(a)) with the MS/MS/MS spectrum of the dianions
formed from 4-amino-3-((4-sulfophenyl)diazenyl)naphthalene-1-sulfonic acid (Fig-
2.10(b)). Interestingly, the major fragment ions at m/z 156.5 (-32 Da), m/z 297.1 and m/z
313.1 corresponding to the loss of SO2, SO3 and SO2- respectively all have the very
similar ion abundance. The result, in this case is a better match than that for the
monsulfonated azodye, possibly because of the absence of positional isomers in the
sample of synthesized amine product. The result hence provides a strong support for the
nucleophilic aromatic substitution proposal for the loss of N2.
MS/MS
MS/MS/MS
Fig-2.10: Comparision of MS/MS spectra of the amine product with that of the MS3
spectrum of the dianions from 4-amino-3-((4-sulfophenyl)diazenyl)naphthalene-1-sulfonic acid (Fig-2.1(e))
A similar experiment was conducted for the corresponding monoanions by
obtaining MS/MS spectrum of the monoanion that was formed in competition from the
HN
SO3
SO3
NH2
SO3
NN
SO3
150 200 250 300m/z
10
20
30
40
50
60
70
80
90
100
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
188.5
156.5
297.1 313.1188.5
156.5
297.1 313.0
296.0221.0
CID (a)
CID (b)
m/z 188.5
CID
48
disulfonated amine product during electrospray ionization (Fig-2.11). The resulting
MS/MS spectrum (Fig-2.11(a)) was compared with the corresponding MS/MS/MS
spectrum of the monoanions from 4-amino-3-((4-sulfophenyl)diazenyl)naphthalene-1-
sulfonate (Fig-2.11(b)). The two spectra are significantly different with one having a
fragment ion at m/z 320 of significant abundance.
This is rather not surprising and arguably, this experiment could explain
and give evidence to the proposed nucleophilic aromatic substitution (Scheme-2.2). In
both cases, monoanions would have formed as a result of deprotonation of any one of the
sulphonic acid residues, resulting in a mixture of two separate monoanions. In the case of
the authentic amine product, the MS/MS spectrum (Fig-2.11(a)) would be the
representative of fragment ions arising from the mixture of two isomeric monoanions.
Whereas, its ambiguous for the monoanions from 4-amino-3-((4-
sulfophenyl)diazenyl)naphthalene-1-sulfonate and the representative MS/MS/MS
spectrum (Figure-2.11(b)) could actually depict only those fragment ions arising from
the monoanions carrying deprotonated sulphonic acid moiety on the naphthyl ring. This
is because the initial CID of the monoanion would have resulted in ions corresponding to
the loss of N2 at m/z 378, only from those ions, containing deprotonated sulphonic acid
moiety on the naphthyl ring. The other isomeric mono anion, with deprotonated
sulphonic acid on the phenyl ring would probably have shown no fragmentation
corresponding to the loss of N2. This is possibly because, electron withdrawing effect of
the sulphonic acid residue in this case, would have deactivated the amine group, and
hence from a possible nucleophilic substitution attack on to the phenyl ring (Scheme-2.7).
49
SO3
NH2
NN
SO3H
CID
-N2
SO3
HN
SO3H
vs
CIDProducts
EWG
SO3H
NH2
NN
SO3
EDG
CID
-N2
SO3H
HN
SO3
CIDProducts
EWG
Scheme-2.7: Substitution nucleophilic mechanism in the monoanions of 4-amino-3-((4-sulfophenyl)diazenyl)naphthalene-1-sulfonate
50
SO3
NH2
NN
SO3H
SO3H
NH2
NN
SO3
+
Fig-2.11: Comparision of MS/MS spectra of the monoanions from disubstituted amine product with that of the MS3 spectrum of the monoanions from 4-amino-3-((4-sulfophenyl)diazenyl) naphthalene-1-sulfonic acid (Fig-2.1(e))
2.2.3.4 Change of nucleophile
The rate of the nucleophilic substitution reactions will be dependent on the
characteristics of the attacking nucleophile and hence the activation barrier for the
reaction, will increase or decrease depending on the strength of the nucleophile. In
general, the order of the nucleophilicity is RNH2 > ROR > ROH, particularly when the
structures of the nucleophiles being compared are otherwise similar.17 Hence, we tested
our proposal by conducting MS/MS (Fig-2.12) on the [M-H]- anion from 4-hydroxy-3-
(phenyldiazenyl)naphthalene-1-sulfonic acid as shown in Fig-2.1(f) , which has OH
moiety replacing the amine at the same position of the naphthalene ring. The spectrum
shows a prominent ion at m/z 327 which corresponds to the [M-H]- molecular ion and a
300 320 340 360 380m/z
20
40
60
80
100
20
40
60
80
100R
elat
ive
Abu
ndan
ce297.8
377.8
319.8
311.8 362.9 373.5338.3 357.3297.8
377.8
375.8
MS/MS
MS/MS/MS
CID (b)
CID (a)
SO3
HN
SO3H
+
SO3
HN
SO3H
CID
m/z 378
51
fragment ion at m/z 247 (-80 Da) corresponding to the loss of SO3. The fragment ion
corresponding to the azo-cleavage was observed at m/z 222 (-105 Da) with low
abundances and hence has been magnified to 100 times it’s original abundance. The
fragment ion at m/z 299 is also only observed at a vanishingly low abundance
corresponding to only 0.22% of the base peak, and that has been amplified to 1000 times
it’s original abundance.
The fragment ion corresponding to the loss of nitrogen is negligible (Fig-
2.12). This result could be attributed to the fact, that the hydroxyl group is a weaker
nucleophile than the amine in the azo dye 4-amino-3-(phenyldiazenyl)naphthalene-1-
sulfonate and thus supports the proposed nucleophilic substitution mechanism in the
latter compound.
180 200 220 240 260 280 300 320 340m/z
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
x1000x100 246.9
326.9
170.8
221.8
298.8
Fig-2.12: CID mass spectrum of negative ions from 4-hydroxy-(phenyldiazenyl) naphthalene-1-sulfonic acid (Fig-1(f))
OH
SO3
NN
CID
52
2.2.3.5 CID of Substituted analogues
Nucleophilic aromatic substitution reactions are generally favoured in
aromatic compounds bearing electron withdrawing groups due to stabilization of negative
charge in the Meisenheimer intermediate and consequent lowering of the activation
barrier.18, 19 To further examine the generality and the mechanism of loss of N2, via the
aromatic substitution mechanism, a para- nitro substituted analogue was subjected to ESI
MS/MS. Figure-2.13 shows the CID mass spectrum of the [M-H]- anion from 4-amino-3-
((4-nitrophenyl)diazenyl)naphthalene-1-sulfonic acid (Fig-2.1(c)) and was recorded at the
same collision energy as the spectrum of the unsubstituted homologue. The molecular
ion is observed at m/z 371 with prominent fragment ions at m/z 307(-64 Da) and m/z
291(-80 Da), corresponding to the basic fragments arising from SO2 and SO3 losses
respectively. The base peak in the spectrum at m/z 263 (-108 Da) corresponds to a
secondary fragment, following consecutive losses of SO3 and N2. Such consecutive loss
of SO3 and N2 were not previously seen in the MS/MS spectrum of the unsubstituted azo
dye.
Interestingly, the spectrum also separated the fragment ion arising from
the loss of anilinyl radical (m/z 234 (-137 Da)) from that arising from consecutive losses
of SO2 and N2 (m/z 279 (-80 Da)). This observation further provides evidence for the
anilinyl radical loss and is consistent with the labeling experiment. Other basic fragment
ions corresponding to the loss of NH3 and N2H2 were observed at m/z 355 and m/z 341.
The azo cleavage fragment ion was observed at m/z 221. Fragment ions corresponding to
the loss of the substituent as NO2 and HNO2 were observed at m/z 325 and m/z 324.
53
In accordance to the substitution prediction, the nitro substitution at the
para position would decrease the barrier for the nucleophilic substitution, thereby
increasing the abundance of product ion corresponding to the loss of N2. Surprisingly, the
fragment ion corresponding to the loss of N2 has similar ion abundance (12%), as
compared with the unsubstituted azodye (15%). Quantitative comparison of fragment ion
abundances between two different fragment ions can be ambiguous because (a)
introduction of new functional group provides competitive pathways for fragmentation
(e.g. –NO2, -HNO2), and (b) under the same collision conditions, the energy imparted to a
molecule depends on the mass of the precursor ion, which in turn affects the fragment ion
abundance.20
Fig-2.13: CID mass spectrum of negative ions from 4-amino-3-((4-nitrophenyl)diazenyl)naphthalene-1-sulfonic acid (Fig-1(c))
NH2
SO3
NN
NO2
150 200 250 300 350m/z
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
262.9
290.9 306.9
370.8
324.8
342.8233.8
278.9247.8151.8 220.8 354.8
CID
54
Further qualitative comparison was obtained by subjecting negative ions
from a para substituted methoxy analogue, 4-amino-3-((4-
methoxyphenyl)diazenyl)naphthalene-1-sulfonic acid (Fig-2.1(b)). The CID spectrum is
presented as Fig-2.14 and shows no loss of N2, even when obtained under the same
conditions as other homologues. This observation is consistent with the destabilization of
the Meisenheimer intermediate by the electron withdrawing methoxy moiety.
Fig-2.14: CID mass spectrum of negative ions from 4-amino-3-((4-methoxyphenyl)diazenyl)naphthalene-1-sulfonic acid (Fig-1(b))
2.2.3.6 Electronic structure calculation
The experimental data discussed above suggest that nitrogen loss from the
azo anions proceed via the intramolecular nucleophilic aromatic substitution reaction
(Scheme-2.2) as opposed to the dissociation-recombination reaction mechanism
(Scheme-2.1). Preliminary electronic structure calculations using B3LYP/6-31+G(d)
level of theory failed to locate Meisenheimer structure (Scheme-2.2(b)) in the proposed
NH2
SO3
NN
OCH3
CID
220 240 260 280 300 320 340m/z
10
20
30
40
50
60
70
80
90
100
Rel
ativ
e A
bund
ance
276.9
356.9
341.8
55
intramolecular aromatic substitution reaction as either a stable intermediate or transition
state. Based on the experimental evidence of tautomerization (Scheme-2.5), a new
aromatic substitution mechanism involving the tautomeric structure was proposed
(Scheme-2.8). The new nucleophilic aromatic substitution mechanism involves initial
tautomerization of parent azo anion (a) to (b), then followed by the attack of the imine
onto the phenyl ring at the ipso position (Scheme-2.8) to form a resonance stabilized
Meisenheimer intermediate (c). The Meisenheimer intermediate would then undergo an
elimination process to form a stable intermediate neutral (d). The resulting intermediate
would then undergo a 1,3-H+ transfer to form the same amine bridged product (e),
consistent with the experimental findings.
NH2
SO3
N
N
SO3
NH
N
HN
SO3
HN NH
N
SO3
N
HN
N
HSO3
HN
(a) (b) (c)
(d)(e)
Scheme-2.8: Aromatic substitution reaction involving tautomeric structure
The calculations were conducted with a model system that employs a
phenyl ring instead of the larger naphthyl ring, to reduce the use of computing time.
Nevertheless, it is expected to be a representative of the larger system.
56
The calculated potential energy surface for the rearrangement of the model
azo anion 4-amino-3-(phenyldiazenyl)benzene-1-sulfonate (Fig-2.1(a)) and subsequent
loss of nitrogen from the anion by the newly proposed mechanism is shown in Fig-2.16,
with energies given relative to the parent anion. The electronic energies of the critical
stationary points are listed in Table-2.1 and the complete structural information of the
critical stationary points are given in Appendix-2. The full Cartesian information of the
stationary points are provided as Appendix-2. In the calculated mechanism the initial
tautomerization from the parent anion to the tautomer IM1 presents a barrier of 39 kJ
mol-1. The energy of the tautomer is 36 kJ mol-1 more than the parent anion. Interestingly,
even though during tautomerization, the aromaticity of the phenyl ring diminishes, the
calculated barrier of 39 kJ mol-1 is four fold lower than the aromatic stabilization energy
(155 kJ mol-1).17 A plausible explanation to support the finding is the presence and
influence of the resonance contributing structure for the hydrazone tautomer. Scheme-2.9
shows the resonance contributing structure of the tautomer.
SO3
NN
HNH
SO3
NN
NHH
Scheme-2.9: Resonance contributing structure of the tautomer
Upon investigation of the structure of the tautomer, it does not clearly
reveal the presence and the influence of the resonance structure as the C-C bond lengths
in the phenyl ring does not seem to have the same length (Fig-2.15 (a)). Nevertheless, the
resonance contributing structure with a strong intramolecular ion-dipole interaction could
57
have possibly reduced the activation barrier of tautomerization. Following the
tautomerization, the nitrogen of the imine, attacks the ipso carbon via the transition state
TS2. This presents a barrier of 197 kJ mol-1 to rearrangement to the stable intermediate,
IM2-Cn1, which lies some 68 kJ mol-1 above the azodye anion minimum. The structure
of TS2 is reminiscent of the proposed structure of the Meisenheimer intermediate, with
the nucleophile –NH completing a near tetrahedral geometry at the ipso position of the
benzene ring (Fig-2.15 (b)).15
(a) IM1 (b) TS1
Fig-2.15: Structures of the Tautomer (1M1) and Meisenheimer transition state (TS1) on the 4-amino-3-(phenyldiazenyl)benzene-1-sulfonate potential energy surface optimized at B3LYP/6-31+G(d) level of theory The intermediate IM2-Cn1 presents two other conformers IM2-Cn2 and
IM2-Cn3, with each conformer differing in the orientation of N=N—H. A transition state,
TS3 was located for the transfer of proton from N=N—H group on to the ipso position
from IM2-Cn2, and thus represents a 1,4- proton transfer. Intrinsic reaction coordinate
58
calculations on this transition state shows that it connects to the intermediate IM3. The
intermediate IM3 is also reminiscent of Meisenheimer intermediate. Intuitively, the
intermediate IM3 would lead to the ion dipole complex IM5 of the proposed product by
simple heterolytic cleavage of C-N bond. No transition state structure could be isolated
for the formation of IM5 from IM3, as isolation of transition state for simple bond
cleavages is often difficult. The ion-dipole complex IM5 presents energy of -155 kJ mol-1
relative to the parent diazo anion. The ion-dipole complex eventually dissociates to the
product Pro. The product Pro presents an energy of -151 kJ mol-1 relative to the parent
azo anion.
The reaction mechanism that could be summarized for 4-amino-3-
(phenyldiazenyl)naphthalene-1-sulfonate encompassing all the intermediates and
transition states from the calculation with the model system is given in Scheme-2.10.
NH2
SO3
NN
SO3
NHN
SO3
HN NHN
SO3
NHN
NH
SO3
NHN
NH
SO3
HN
N2
HN
Scheme-2.10: Calculated reaction mechanism-1 for 4-amino-3-(phenyldiazenyl) naphthalene-1-sulfonate
59
The other conformer IM2-Cn3 connects an alternative transition state TS4,
representating a 1,5-proton transfer on to the amine from the N=N−H. This presents a
barrier of 248 kJ mol-1. Intrinsic reaction coordinate calculations on the transition state
connect it to a charge separated intermediate minimum IM4, with an optimized energy of
189 kJ mol-1 relative to the parent anion. This charge separated intermediate IM4
undergoes a 1,3-proton transfer, through a transition state TS5 to the proposed product
Pro.
The other reaction mechanism that could be summarized for 4-amino-3-
(phenyldiazenyl)naphthalene-1-sulfonate encompassing all the intermediates and
transition states from the calculation with the model system is given in Scheme-2.11.
NH2
SO3
NN
SO3
NHN
HN
SO3
HN NHN
SO3
NHN N
H
SO3
HN-N2
H
SO3
HN
Scheme-2.11: Calculated reaction mechanism-2 for 4-amino-3-(phenyldiazenyl) naphthalene-1-sulfonate
60
196.8183.3
-151.2
78.7
35.8
295.9
349.9
365.0
285.6
67.7
0.0
278.7
39.5
68.9
247.9186.8
188.5
-155.8
Reaction Coordinate
kJ/m
ole
NH2
SO3-
NN
NH2
SO3-
+ +N2
SO3-
NH2
N
+N
SO3
HNNN
H
SO3-
NHN
NH
+ so3
NNHNH
so3
NN
HHN
so3
NHN
NH
so3
NNHN
H
SO3
NHN
NH
so3
NNHN
H
so3
HN H+ N2
SO3-
HN
N2
SO3-
HN
N2+
TS1
IM1
TS2
IM2-Cn1
IM2-Cn2
IM2-Cn3
TS3
IM3
TS4
IM4 TS5
Tau-pro
azo-pro2
azo-pro1
IM6
IM5
Pro
SO3
NHN
NH
so3
H2NN2
so3
H2N+ N2
SO3-
NNN
H H
Fig-2.16: Reaction coordinate diagram for the intramolecular rearrangement of the model diazo anion, 4-amino-3-(phenyldiazenyl)benzene-1-sulfonate model system calculated at B3LYP/6-31+G(d) level of theory. All energies are given in kJ mol-1. The uncorrected energies (not including (ZPE)) place TS4 higher than IM6 by 4.1 kJ mol-1.
61
Table-2.1: Optimized stationary points calculated for the loss of N2 from 4-amino-3-(phenyldiazenyl)benzenesulfonate anion (Electronic energy zero-point energy, relative energy and imaginary frequency calculated at B3LYP/6-31+G(d) level of theory)
Structure
Energy
Hartrees
Zero-point Energy
Hartrees
Relative energy
kJ mol-1
4-amino-3
(phenyldiazenyl)
benzenesulfonate
-1251.44306
0.20948
0.0
TS1 (-1453 cm-1
) -1251.42392
0.20539
39.5
IM1 -1251.43005
0.21009
35.8
TS2 (-370 cm-1
) -1251.36715
0.20852
196.8
IM2-Cn1 -1251.41741
0.20963
67.7
IM2-Cn2 -1251.41625
0.20893
68.9
IM2-Cn3 -1251.41271
0.20911
78.7
TS3 (-873 cm-1
) -1251.29701
0.20247
365.0
TS4 (-472 cm-1
) -1251.34418
0.20502
247.9
IM3 -1251.30546
0.20517
349.9
IM4 -1251.36796
0.20554
186.8
TS5 (-820 cm-1
) -1251.36501
0.20122
183.3
IM5 -1251.49873
0.20581
-155.8
IM6 -1251.36659
0.20481
188.5
Azo-pro1 -1251.32471
0.20382
295.9
Azo-pro2 -1251.32437
0.19956
285.6
Tau-pro -1251.33019
0.20276
278.7
Pro -1251.49676
0.20559
-151.2
62
Interestingly, from these calculations, the transition state barriers TS3 and
TS4, appear to dictate the energetics of the reaction and not the transition state that
involves the formation of Meisenheimer structure TS2, which was initially thought to be
the rate determining step. The calculation also suggests that the mechanism involving the
formation of charged separated intermediate IM4 (Scheme-2.11) could be the most
thermodynamically favoured pathway, as the transition TS4 in the mechanism presents a
lower barrier than the barrier TS3 in the other calculated mechanism (Scheme-2.10).
Calculations were also conducted for the tautomeric cleavage and azo
cleavage process. The products for tautomeric cleavage is represented by Tau-Pro with
its energy at 279 kJ mol-1, and that of the azo cleavage (Azo-Pro) at 296 kJ mol-1. It
could be seem that these pathways are endothermic while the rearrangement to the amine,
effecting the loss of nitrogen is exothermic (Fig-2.16).
The calculation could also suggest that the absence of fragment ion
corresponding to the loss of nitrogen for 4-hydroxy-3-(phenyldiazenyl)naphthalene-1-
sulfonate could be due to two important properties of the hydroxyl substituent. The
corresponding transition state TS2 could present a higher barrier as hydroxyl analogue is
less nucleophilic than the amine counterpart. Also, the transition state, corresponding to
the formation of the charged separated intermediate TS4, could present a higher barrier as
the basicity of the hydroxyl substituent is lower than the amine counterpart.
Initial calculations, were performed to investigate the effect of hydroxyl
moiety, by replacing the amine to a hydroxyl group in the model system (Fig-2.17). The
electronic energies of the critical stationary points are given in Appendix-2. The full
Cartesian information of the stationary points are provided as Appendix-2. Surprisingly,
63
the tautomerization occurs over a barrier of 9 kJ mol-1 (Hyd-TS1), which is four fold
lower than for the 4-amino-3-(phenyldiazenyl)benzene-1-sulfonate (Fig-2.17). This
explains why the abundance of the tautomeric products (m/z 222) is much higher for the
4-hydroxy-(phenyldiazenyl) naphthalene-1-sulfonate (Fig-2.12) as compared with 4-
amino-(phenyldiazenyl) naphthalene-1-sulfonate (Fig-2.2). The plausible explanation
could be that the hydroxyl substituent is better proton donor than the amine counterpart,
which effectively could decrease the activation barrier. Adding to the above result, the
energy of the tautomer also presents lower energy (2.4 kJ mol-1), which is significantly
lower than that found for the 4-amino-(phenyldiazenyl) naphthalene-1-sulfonate (Fig-
2.16).
The Meisenheimer transition state presents comparatively similar barrier
of 205 kJ mol-1 (Fig-2.17) as compared with the 4-amino-3-(phenyldiazenyl)benzene-1-
sulfonate (TS2, Fig-2.16). A rearrangement to the stable intermediate, Hyd-IM2-Cn1
occurs following the Meisenheimer transition state and that the intermediate lies some 89
kJ mol-1 above the parent anion. Here again the intermediate Hyd-IM2-Cn1 presents two
other conformers Hyd-IM2-Cn2 and Hyd-IM2-Cn3, with each conformer differing in
the orientation of N=N—H. A transition state, Hyd-TS3 was located for the transfer of
proton from N=N—H group on to the ipso position from Hyd-IM2-Cn2. The barrier to
this process, again is very similar to that of 4-amino-(phenyldiazenyl)benzene-1-sulfonate
(TS3, Fig-2.16) leading to the formation of the intermediate Hyd-IM3. The intermediate
Hyd-IM3 leads to the proposed product, which is -128 kJ mol-1 relative to the parent azo
anion. The result suggests that this pathway is highly unlikely to effect the loss of N2 due
to the high transition barrier, represented by Hyd-TS3.
64
Nevertheless, the reaction mechanism that could be summarized for 4-
hydroxy-3-(naphthyldiazenyl)naphthalene-1-sulfonate encompassing all the intermediates
and transition states from the calculation with the model system is given in Scheme-2.12.
OH
SO3
NN
SO3
O
N
SO3
O NH
N
SO3
N
O
NH
SO3
N
O
NH
SO3
O
N2
HN
Scheme-2.12: Calculated reaction mechanism-1 for 4-hydroxy-3(phenyldiazenyl) naphthalene-1-sulfonate
The transition state which was the rate determining transition state (TS4,
Fig-(2.16)) in 4-amino-3(phenyldiazenyl)benzene-1-sulfonate potential energy surface, in
the 4-hydroxy-3(phenyldiazenyl)benzene-1-sulfonate calculation Hyd-TS4, presents a
barrier of 335 kJ mol-1. Surprisingly, intrinsic reaction coordinate calculation on the
transition state connects it to a benzyne-like intermediate with a loss of phenol and
nitrogen as neutrals (Hyd-Pro2) as opposed to the loss of just the N2 in the 4-amino-
3(phenyldiazenyl)benzene-1-sulfonate. The process of the loss of N2 and phenol would
involve a cyclic cleavage reaction and the optimized energy of the products formed were
196 kJ mol-1 relative to the parent anion (Fig-2.17).
65
The other reaction mechanism that could be summarized for 4-hydroxy-3-
(naphthyldiazenyl)naphthalene-1-sulfonate encompassing all the intermediates and
transition states from the calculation with the model system is given in Scheme-2.13.
OH
SO3
NN
SO3
ON
HN
SO3
O NHN
SO3
NO N
H
-N2SO3 OH
+
Scheme-2.13: Calculated reaction mechanism-2 for 4-hydroxy-3(phenyldiazenyl) naphthalene-1-sulfonate
An alternative explanation for the loss of 28 Da could be the loss of CO arising
from the phenoxide isomer of the parent anion. Computational data (shown in chapter 3)
for dissociation of phenoxide indicate that CO loss occurs over a barrier of 439 kJ mol-1.
This is similar to the energetic requirement for the loss of N2 (381 kJ mol-1Fig-2.17,
TS3). Thus some participation of CO loss in the formation of the fragment ion at m/z
299 in 4-hydroxy-3(phenyldiazenyl) naphthalene-1-sulfonate cannot be excluded.
66
204.9
378.1
-128.4
195.7
119.2
-132.7
334.5
2.4
99.292.489.3
8.70.0
381.4
Reaction Coordinate
kJ
/mo
le
OH
SO3-
NN
SO3
ONN
H
SO3-
ONN
H
so3
NNHO
so3
NN
HO
so3
NO
NH
so3
NNO
H
SO3
NO
NH
SO3-
O
N2+
Hyd-TS1
Hyd-IM1
Hyd-TS2
Hyd-IM2-Cn1 Hyd-IM2-Cn2Hyd-IM2-Cn3
Hyd-IM3
Hyd-Pro
Hyd-TS4Hyd-TS3
SO3
NO
NH
Hyd-Pro-2
SO3
O
NN
H
SO3
+
OH
+ N2
SO3-
O
N2
Hyd-IM5
SO3OH
N2
Hyd-IM-New
Fig-2.17: Reaction coordinate diagram for the intramolecular rearrangement of the 4-hydroxy-(phenyldiazenyl)benzene-1-sulfonate model system calculated at B3LYP/6-31+G(d) level of theory. All energies are given in kJ mol-1.
67
In regards to the substituted analogues, rationalizing the result would be
rather difficult particularly because the Meisenheimer transition state, TS2 does not
represent the rate determining transition state. On consideration, in the methoxy analogue
the charge separated intermediate IM4 could be more stabilized due to the electron
donating nature of the methoxy substituent. This could present a counter effect on the
driving force to form the stabilized amine product and hence the transition state barrier
TS4 could present a higher energy barrier. Nevertheless, the Meisenheimer transition
state TS2, could present a lower barrier for the nitro substituted analogue and a higher
barrier for the methoxy analogue. Being, the first transition state, apart from the TS1,
which significantly requires a very high energy (200 kJ mol-1) it could largely affect the
proceeding of the rearrangement reaction. These facts could plausibly explain why the
methoxy analogue showed no rearrangement to effect the loss of nitrogen. More over on
close examination of the methoxy spectrum (Fig-2.14), we could see no fragment ions
corresponding to the loss of N2 and the phenyl radical and anilinyl radical. This suggests
that the competitive fragmentation pathway leading to the loss of methoxy substituent
(m/z 342) and sulfonate substituents (m/z 277) could have complicated other observed
fragmentation pathways (Fig-2.14). As well as for the nitro substituted analogue,
competitive fragmentation pathway with lower barriers could have largely reduced the
ion abundance that corresponds to the loss of nitrogen.
Generally in dianions, direct dissociation pathways are preferred and
rearrangement pathways are hindered due to Coulombic repulsions.21 Hence, we
conducted a prelimary calculation, to understand the influence of the Coulombic
68
repulsion on the identified rearrangement pathway. The various intermediates from the
calculated pathways of 4-amino-3-(phenyldiazenyl)benzene-1-sulfonate model were
optimized as stationary points with an additional sulphonate moiety on the other benzene
ring, under the same level of theory. The electronic energies of the critical stationary
points are given in Appendix-2. The full Cartesian information of the calculated
stationary points are provided as Appendix-2. The Coulombic repulsion energy for each
stationary points were then calculated by using the formula kq1q2/r2, where k was
assumed as permetivity of vaccum, the data for which is presented in Scheme-2.14.
69
Distance = 11.66 Å
Distance= 11.79 Å
Energy = 0 kJ mol-1
Energy = 34 kJ mol-1
NH2
SO3
NN
SO3
NHN
HN
SO3
HN NHN
SO3
NHN
NH
SO3
NHN
NH
SO3
HN
N2
SO3
NHN N
H
SO3
HN
N2
H
SO3
HN
Distance = 11.28 Å
Energy = 79 kJ mol-1
SO3 SO3
SO3
SO3 SO3SO3
SO3
SO3
SO3
Repulsion energy = 0 kJ mol-1
Repulsion energy = -2 kJ mol-1
Repulsion energy= 4 kJ mol-1Repulsion energy = 3 kJ mol-1
Distance = 11.33 Å
Distance = 11.21 Å
Energy = 84 kJ mol-1
Repulsion energy = 4 kJ mol-1
Energy = -142 kJ mol-1
Repulsion energy = 3 kJ mol-1
Distance = 11.33 Å
Energy = -142 kJ mol-1
DI-IM1
DI-IM2Cn2
DI-IM2Cn3
DI-Pro
DI-Pro
DI-TS1
Distance = 11.01 Å
Energy = 165 kJ mol-1
Repulsion energy = 6 kJ mol-1DI-IM6
Scheme-2.14: Preliminary calculation on the dianion system
70
The result suggest that the distance between the two sulfonate substituent
does not change much, from each stationary points in the two calculated pathways, thus
suggesting that Coulombic repulsion would play no major role in the rearrangement and
that the rearrangement is feasible in the dianions.
2.3 Conclusion
The combined experimental and theoretical study has revealed an
interesting rearrangement that effects the loss of azo moiety as nitrogen, upon CID of azo
dye anions. Initial substituent and nucleophile change studies supported a direct
intramolecular nucleophilic aromatic substitution effecting the loss of N2 and that the
energetics of the rearrangement is dictated by the transition state corresponding to the
nucleophilic substitution reaction. The complementary computational study however
suggested that the rearrangement proceeds via an initial tautomerization, followed by
nucleophilic aromatic substitution reaction and that the course of the reaction is more
complex with other transition states providing the rate determining step. Moreover, the
complementary computational studies on the nucleophile changed analogue reveals a
more complex reaction manifold and that does not follow the logical and straight forward
conclusions that could be derived from textbooks. The rearrangement was surprisingly
observed for the dianion, and that the preliminary calculation on the system suggests that
the reaction would proceed without any influence from Coulombic repulsion.
71
2.4 Experimental
2.4.1 Mass spectrometry
Standard solutions of azo dyes (10 µM) were prepared in aqueous
acetonitrile (50% v/v) solution. A few drops of aqueous ammonia (48% v/v) were added
to these solutions to aid deprotonation of the azo dyes. Mass spectra were obtained using
ThermoFinnigan LTQ linear ion-trap mass spectrometer (Thermo Electron Corporation,
San Jose, USA). Spectra were obtained by infusion of the standard solution (10µL/min),
typical settings were cone voltage (3.51 kV), capillary voltage (-5.89 V), source
temperature (270oC). Helium was used as the collision and buffer gas at a pressure of (7.6
x 10-6 torr).The dianion spectrum was obtained under the same settings except the source
temperature was set at 140oC to minimize decomposition in the source. The spectrum
presented results from the average of at least 50 scans and was baseline corrected to 5%
using Xcalibur software package (Thermo Electron Corporation, San Jose, USA).
2.4.2 Synthesis of azo compounds
All the azo dye compounds were prepared and characterised by
Christopher Gordon from the Department of Chemistry, University of Wollongong.g A
standardized procedure for the synthesis includes:
To a stirring solution of aniline (0.15 mL, 1.61 mmol) in HCl (4 M, 5.00
mL) at 0oC was added dropwise a solution of sodium nitrite (0.13 g, 1.93 mmol) in
distilled water (5 mL). The resulting mixture was stirred at 0oC for 15 minutes before the
g Gordon, C. J., Structure based design and synthesis of small molecules human immuno deficiency virus type 1 entegre inhibitors, in School of Chemistry. 2007, University of Wollongong, Wollongong.
72
corresponding naphthalene sulfonic acid was added (Fig-2.1). The mixture was then
vigorously stirred at room temperature for a further 30 minutes prior to the addition of
NaOH (2 M, 10 mL). The resulting coloured precipitate was collected and purified via
recrystalliation (10:10:1 acetone/EtOH/2M HCl) to effect the formation of brightly
coloured azo dyes as solids. These compounds were characterized by their melting point
(m.p.), 1H-NMR and 13C-NMR.
2.4.3 Synthesis of authentic amine compounds
A stirred suspension of N-phenyl-1-naphthleneamine (2.00 g, 9.13 mmol)
in H2O (5 mL) was cooled to 0 °C to which conc. H2SO4 (10 mL) was added dropwise.
The resulting mixture was stirred at 80 °C for 16 h after which the reaction was quenched
with NaHCO3(aq), extracted with EtOAc (4 × 25 mL), dried (MgSO4), and concentrated in
vacuo. The resulting brown oil was subjected to preparative layer chromatography (1:1,
EtOAc:MeOH) to afford both the monosulfonated and disulfonated products (0.15g, 4%)
as a dark brown viscous oil.
2.4.4 Calculations
Geometric optimizations were carried out with the B3LYP method22, 23
using 6-31+G(d) basis set within the Gaussian suite of programs.24 All stationary points
on the potential energy surface were characterized as either minima (no imaginary
frequencies) or transition state (one imaginary frequency) by calculation of frequency
using analytical gradient procedure. Frequency calculations provided zero-point energies,
which were added to the calculated energy. The minima connected by a given transition
state were confirmed by inspection of the animated imaginary frequency using the Gauss
73
view package 3.0 (Gaussian, Inc, Pittsburgh, USA) and by intrinsic reaction coordinate
calculation.25, 26
74
References for chapter two
1. Kulkarni, S. V.; Blackwell, C. D.; Blackard, A. I.; Stack-house, C. W.; Alexander,
M. W., Textile Dyeing Operations. Chap. G, Moyes Publications: Park Ridge, NJ, 1986.
2. Voyksner, K.; Straub, R.; Keever, J., Environ. Sci. Technol. 1993, 27, 1665-1672. 3. Cooks, J.; Thurnhear, T.; Kohler-Staub, D.; Galll, R.; Grossbacher, H., Swiss.
Biotech. 1988, 4, 14-17. 4. Venkataraman, K., The analytical chemistry of synthetic dyes. Wiley-Interscience:
1977. 5. Mattias, A.; Williams, A. E.; Games, D. E.; Jackson, A. H., Org. Mass Spectrom.
1976, 11, 266. 6. Straub, R.; Voyksner, R. D.; Keever, J. K., J. Chromatogr. 1992, 627, 173. 7. Richardson, S. D.; McGuire, J. M.; Thructon, A. D.; Baughman, G. L., Org. Mass
Spectrom. 1992, 27, 289. 8. Sullivan, A. G.; Gaskell, S. J., Rapid Commun. Mass Spectrom. 1997, 11, 803. 9. Panell, L. K.; Sokoloski, E. A.; Fales, H. M., Anal. Chem. 1985, 57, 1060. 10. Monaghan, J.J.; Baber, M.; Bordoli, R. S.; Sedgwick, R. D.; Tyler, A. N., Int. J.
Org. Mass Spectrom. Ion Phys. 1983, 46, 447. 11. Ballard, J. M.; Betowski, L. D., Anal. Chem. 1984, 56, 2604. 12. Sullivan, A. G., Garner, R., and Gaskell, S. J., Rapid Commun. Mass Spectrom.
1998, 12, 1207-1215. 13. Bowie, J. H.; Lewis, G. E., J. and Cooks, R. G., Chem. Soc. (B) 1967, 621. 14. Bowie, J. H., The fragmentations of even-electron organic negative ions. Mass
Spectrom. Rev. 1990, 9, 349-379. 15. Giroldo, T. A.; Xavier, L. A.; Riveros, J. A., Angew. Chem. Int. Ed 2004, 43,
3588-3590. 16. Binkley, R. W.; Flechtner, T. W.; Teversz, M. J. S.; Winnik, W.; Zhong, B., Org.
Mass Spectrom. 1993, 28, 769-772.
75
17. March, J., Advanced organic chemistry: reactions, mechanisms, and structure. 4 ed.; Wiley, c1992: New York, 1929; p 349 .
18. Meisenheimer, J., Liebigs Ann. Chem. 1902, 323, 205. 19. Artamkina, G. A.; Egorov, M. P.; Beletskaya, I. P., Chem. Rev. 1982, 82, 427. 20. Downard, K., Mass spectrometry: A foundation course. Royal society of
Chemistry: Cambridge, 2004. 21. Schroder, D., Angew. Chem. Int. Ed 2004, 43, 1329. 22. Becke, A. D., J. Chem. Phys. 1993, 98, 1372. 23. Lee, C. T.; Yang, W. T., Parr, R. G., Phys. Rev. B: Condens. Matter 1988, 37, 785. 24. Gaussian 03 (Revision C.02). Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.;
Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, Jr., J. A.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; and Pople, J. A.; Gaussian 03, Revision
C.02, Gaussian, Inc.: Wallingford CT, 2004. 25. Gonzalez, C.; Schlegel, H. B., J. Chem. Phys. 1989, 90, 2154. 26. Gonzalez, C.; Schlegel, H. B., J. Phys. Chem. 1990, 94, 5523.
76
CHAPTER THREE: COMPUTATIONAL INVESTIGATION
OF THE REARRANGEMENT AND FRAGMENTATION OF
PHENOXIDE ANION IN THE GAS-PHASE
Abstract
O
CO
CO
+ CO
H HCO
CO
CO
HCO
CO
CO
H
CO
O
O
O
CO
CH
O O O
OC
O
H OH C
O
The rearrangement and fragmentation of phenoxide anion in the gas-phase was
studied by electronic structure calculation carried out at B3LYP/6-311++G(d,p) level of
theory. The study investigated previously reported Collision-Induced Dissociation (CID)
studies of phenoxide anions, where product ions consistent with the loss of CO were
observed. The data from another study indicating the involvement of benzene-oxide and
oxepin intermediates during the fragmentation was also investigated. Primarily, the
77
electronic structure calculations reveal that the loss of CO occurs via two competing
reaction pathways involving ketene like intermediates and transition states. The
computational data also reveals the existence of rearrangement pathway of phenoxide
anion to benzene-oxide and oxepin structures eventually effecting the loss of CO.
78
3.1 Introduction
Phenols and related poly phenols have been used in the medical industry
for nearly over two centuries. The first use of phenol in the field of medicine was as an
antiseptic and it was Sir Joseph Lister (1827-1912) who showed that phenols can be used
as an antiseptic during surgery. Since then, phenolic compounds have been used in the
production of variety of useful commodities such as asprin, weed killer, wood
preservatives, disinfectants and bakelite.1
As a result of their extensive industrial and domestic use, large amounts of
synthetic phenols find their way into environmental waterways. Phenols, if present in
large quantities in environmental water-ways are known to be toxic for aquatic life.2
Phenols are also known to cause a number of health effects in humans. Some of the
reported health effects include cardiovascular effects, respiratory distress, metabolic
acidosis, renal failure, neurological effects, shock, coma and death. Gastrointestinal
effects such as nausea and vomiting have been reported as major health effects. Dermal
effects such as dermal inflammation and erythema are also very common upon exposure.
Moreover, exposures to some phenols are known to cause permanent genetic damage.h
Interestingly phenolic compounds are also biologically produced and
secreted by all living forms, including plants and humans. The phenols secreted by plants
are popularly known as polyphenols and they contain multiple chains of aromatic rings
with the hydroxyl moiety. Food sources that are rich in polyphenols include onion, apple,
tea, red wine, red grapes, grape juice, strawberries, raspberries, blueberries, cranberries,
and certain nuts. 3
h International Programme on Chemical Safety (IPCS) (1999). Phenol. Poisons Information Monograph. PIM 412.
79
For many years polyphenols as a dietary component was considered
antinutritive, and was thought to account only for the colour and flavour of certain food
stuffs. Currently polyphenols as dietary components are classified under phytonutrients
which refers to those bioactive components that promote significant positive health
effects in humans.3 Polyphenols basically protect plants and humans from oxidative
damage. These polyphenols are also known to block specific enzymes that cause
inflammation and allergies. i ,4,5 They also help the liver detoxify and inhibit specific
enzymes such as the angiotensin-converting enzyme (ACE) that raises blood pressure.
Polyphenols can be classified as non-flavonoids and flavonoids. j However, only the
flavonoids quercetin and phytoestrogens have been extensively studied. Quercetin was
found to possess anti-allergy, anti-inflammatory, immune modulating, anti-viral,
anticancer, lipid antioxidant and gastro-protective properties.k Phytoestrogens are those
flavonoid compounds that have the similar structure to mammalian estrogens. Food
sources that are rich in phytoestrogens are nuts, oil seeds, soy beans, cereals, breads,
legumes and flax seeds. Studies have shown that eating foods containing phytoestrogens
can help to reduce the symptoms of menopause and cardiovascular diseases.l,m,n However
phytoestrogens are also known to be endocrine-disrupting chemicals (EDC) with strong
anti-estrogenic activity.o
i Hertog, M.G.; Feskens. E. J.; Hollman. P. C.; Katan. M. B.; Kromhout. D., Lancet., 1993, 342, 8878. j Kinsell, J. E.; Frankel, E.; German, B.; Kanner, J., Food Technology, 1993, 47, 85. k Murray, R. G.; Granner, D. K.; Mayes, P. A.; Rodwell, V. W., Harper’s Biochemistry. 23 ed.; Appleton and Lange, New York, 1929; p 196. l Osaski, A. L.; Kennelly, E. J. Phytother. Res. 2003, 17, 845. m Linseisen, L.; Pillar, R.; Hermann, S.; Change-Claude, J., Int. J. Cancer 2004, 110, 284. n Bingham, S. A.; Atkinson, C.; Liggins, J.; Bluck, L.; Coward, A., Br. J. Nutr. 1998, 79, 393. o Barrett, J., Environ. Health Perspect. 1996, 39, 104.
80
Such huge interest in the phenolic compounds led to several studies on the
analysis and detection of phenols and polyphenols from biological and environmental
samples by using a combination of chromatographic and mass spectrometric techniques
or perhaps by using tandem mass spectrometry.p,6,q,r,s
The continuing interest in analysis and detection of phenolic compounds
from environmental and biological samples over the past two decades led to a numerous
studies, aimed at obtaining further structural information to better characterize phenolic
compounds. Numerous Collision-Induced Dissociation (CID) experiments on phenoxide
anions were conducted to enhance the understanding of basic fragmentation mechanism
of phenoxide anion, which as such has provided characteristic fragmentation finger
prints for identification and detections of phenolic compounds from biological and
environmental samples.7-11 Interestingly, in all the CID studies of phenoxide anion,
phenoxide anion was consistently found to fragment via a loss of 28 Da corresponding to
the loss of CO. Other prominent losses were the loss of H2O, C2H4 leading to the
formation of benzyne and cyclobutenone anions.7-11 This facile loss of CO was also
observed in the dissociation of polyphenolic compounds such as catechol, resorcinol and
hydroquinones.12-14
Binkley and co-workers proposed a mechanism for the facile loss of CO
involving the loss of the ipso carbon (Scheme-3.1).11 In the proposed mechanism, the
resonance structure (B) undergoes a ring closure reaction to form a bicyclic structure (C).
The ring closure reaction is perhaps a nucleophilic reaction, where the carbon at the ortho
p Globig, D.; Weickhardt, C., Anal. BioAnal. Chem. 2003, 377, 1124. q Kang, J.; Hick, L. A.; Price, W. E., Rapid Commun. Mass Spectrom. 2007, 21, 4065. r Kang, J.; Hick, L. A.; Price, W. E., Rapid Commun. Mass Spectrom. 2007, 21, 857. s Kang, J.; Price, W. E.; Hick, L. A, Rapid Commun. Mass Spectrom. 2006, 20, 2411.
81
position attacks an equivalent ortho carbon. The structure (C) eventually undergoes a ring
opening reaction to form the cyclopenta-2,4-dienyl(oxo)methanide anion (D). The
methanide anion subsequently forms the resonance stabilised cyclopentadienyl anion (E)
via a loss of CO. Even, though the transition states may demand high energy input, the
driving force for this process could be the formation of resonance stabilised
cyclopentadienyl anion and stable CO neutral (Scheme-3.1).11
O O O
+ CO
A B C D
C O
E
Scheme-3.1: Binkley and coworker’s mechanism of phenoxide fragmentation11
Interestingly, it was a CID study of phenoxy ethoxide anion by Bowie and
co-workers that provided the evidence for Binkley’s mechanism. In the study, it was
hypothesized that the phenoxy ethoxide anion undergoes a Smiles rearrangement in the
gas-phase i.e. an intramolecular nucleophilic aromatic substitution reaction at the ipso
position of the aromatic ring (Scheme-3.2).
O
OO
O
O
O
Scheme-3.2: Smiles rearrangement in the Gas-Phase
The CID of phenoxy ethoxide anion, resulted in the formation of a product
ion at m/z 93 corresponding the phenoxide anion (Scheme-3.3). The formation of
phenoxide anion during fragmentation was confirmed by comparing the CID mass
spectrum of the product ion at m/z 93 with that of
82
the authentic phenoxide anion.
O
OO
O
O
Smiles rearrangement
O CID_
Scheme-3.3: Fragmentation of phenoxy ethoxide anion
To probe the occurrence of Smiles rearrangement in the gas-phase, Bowie
and co-workers conducted labeling experiments involving, the isotopic labeling of the
terminal oxygen atom with 18O-oxygen in phenoxy ethoxide anion (Ph16O(CH2)218O-) and
then subjecting it to CID. The product ion spectrum obtained after CID, contained equal
proportions of the two possible phenoxide fragment ions , one at m/z 93 (Ph16O-), and the
other at m/z 95 (Ph18O-) (Fig-3.1), thus providing compelling evidence for the occurrence
of Smiles rearrangement in the gas-phase (Scheme-3.4).15
83
Fig-3.1: CID Mass Spectrum of the labeled ethoxide anion (Ph16O(CH2)218O-)15
O
O1818O
O
O18
O
CID
m/z 93
Smiles rearrangement
O CID
18O
m/z 95
Scheme-3.4: Fragmentation of the labeled phenoxy ethoxide anion (Ph16O(CH2)218O-)
Furthermore, to probe into the reaction specificity at the ipso position of
the aromatic ring, the ipso carbon of PhO(CH2)2O- was labeled with 13C-carbon and then
was subjected to CID. The product phenoxide ion obtained from collision-induced
dissociation of the labeled phenoxy ethoxide anion, upon further collisional activation,
84
fragmented exclusively by the loss of 13CO thus providing compelling evidence for the
reaction specificity (Scheme-3.5).15
Scheme-3.5: Fragmentation of the 13C labeled phenoxy ethoxide anion (PhO(CH2)2O-)
As such, both labelling studies provided evidence for the Smiles
rearrangement, but in addition the results provided evidence for the loss of ipso carbon as
CO during the fragmentation of the phenoxide anion. Infact, these results were used by
Binkley and co-workers in conjunction with their study, to explore and propose the
mechanism for the fragmentation of phenoxide anion involving the ipso carbon, leading
to formation of cyclopentadienyl anion via a loss of CO (Scheme-3.1).
In a recent study on the dissociation of perbenzoate anions by Blanksby
and co-workers, fragment ions corresponding to the formation of phenoxide anion were
observed following the loss of CO2.16 The spectrum obtained after further dissociation of
the fragment ion matched with that of the authentic phenoxide anion. Even though,
experimental evidence supported the formation of phenoxide anion in the rearrangement
13 O
O
13
O
O
O
13O
CID
m/z 94
Smiles rearrangement
O CID
13O
m/z 94
CID CID13CO13CO
C5H5- C5H5
-
85
process, the complementary computational study on the rearrangement surprisingly,
revealed that the facile loss of CO2 occurs via an intramolecular epoxidation of benzene
ring, leading to the formation of benzene-oxide and oxepin as intermediates (Scheme-
3.6).The result suggests that the benzene-oxide and oxepin intermediates may be linked
via facile rearrangement to phenoxide anion in the gas-phase.16
OOO
ortho
ipso
OO
O OO
O OCO2
OO
OOOO OC
O
O
CO2O
Scheme-3.6: Fragmentation of Perbenzoate anion16
Our study primarily aims at elucidating the mechanism for the loss of CO from
phenoxide anion by computational methods but in addition we aim to elucidate the
possible rearrangement of benzene-oxide and oxepin intermediates to phenoxide anion.
3.2 Materials and methods
Geometric optimizations were carried out with the B3LYP method17, 18
using 6-311++G(d,p) basis set within the Gaussian suite of programs.19 All stationary
points on the potential energy surface were characterized as either minima (no imaginary
frequencies) or transition state (one imaginary frequency) by calculation of frequency
using analytical gradient procedure. Frequency calculations provided zero-point energies,
which were added to the calculated energy. The minima connected by a given transition
state were confirmed by inspection of the animated imaginary frequency using the Gauss
86
view package 3.0 (Gaussian, Inc, Pittsburgh, USA) and by intrinsic reaction coordinate
calculation.20, 21
3.3 Results and discussion
In an effort to explore the validity of the mechanism proposed by Binkley
and co-workers, the structures in Scheme-3.1 were optimized at the B3LYP/6-311++G(d,
p) level of theory. The bicyclic structure in Scheme-3.1(c) however could not be
optimized either as a stable minima or transition state. Hence, a new mechanism was
proposed, which involves ketene as an intermediate (Scheme-3.7). In the newly proposed
mechanism, the phenoxide anion (A), ring opens to form a ketene intermediate (B). The
ketene subsequently undergoes a ring closure reaction to form cyclopenta-2,4-
dienyl(oxo)methanide anion (C). The anion subsequently undergoes a decarbonylation
reaction to give the observed cyclo pentadienyl anion (Scheme-3.7).
OC
O CO
+ CO
A B C D
Scheme-3.7: Proposed fragmentation pathway for phenoxide decomposition
Electronic structure calculations have been performed to investigate the
mechanism in detail. The calculated potential energy for the fragmentation of the
phenoxide anion is shown in Figure-3.2 with energies given relative to the phenoxide
anion. The electronic energies of the critical stationary points are listed in Table-3.1 with
their molecular structure provided in Figure-3.3. The full Cartesian coordinates of the
87
stationary points are provided in Appendix-3. The energies of the various intermediates
and transition states are given relative to the phenoxide anion
88
Fig-3.2: Reaction coordinate diagram for the fragmentation of the phenoxide anion in the gas-phase calculated at B3LYP/6-311++G(d,p) level of theory. All energies given in kJ mol-1.
0.0
438.7403.4
139.6
390.0
352.9371.6
396.7
359.6
166.4 151.5
TS1
IM1 TS2IM2
TS3
IM3
TS4 TS5
P1
P2
+
89
(a) Phenoxide (b) TS1
(c) IM1 (d) TS2
(e) IM2 (f) TS3
90
(g) TS4 (h) IM3
(i) TS5 (j) P2
91
(k) P1
Fig-3.3: Structures of the stationary points on the phenoxide potential energy surface optimized at B3LYP/6-311++G(d,p) level of theory. All lengths given in angstroms and angles in degree. All the dihedral angles (Ø) are defined with respect to the plane below, containing the three carbon atoms. Considering the phenoxide fragmentation via ketene like intermediate, the
phenoxide anion undergoes a ring opening reaction via the transition state TS1 (Fig-3.2).
The transition state presents a barrier to 397 kJ mol-1 above the entrance channel (Fig-
3.2). From the molecular structure of TS1 (Fig-3.3(b)), a rather surprising dihedral angle
of 96° for the terminal C=C bond about the plane of the aromatic ring was observed. This
suggests that the ring opening reaction is just not a simple heterolytic cleavage, but also
encompasses rotation of the terminal C=C out of the plane of the ring. IRC calculation on
the transition state TS1 locates a ketene intermediate, IM1 (Fig-3.2), in which the
terminal C=C bond has rotated nearly 180° from its original position in phenoxide (Fig-
3.3(c)). Following the formation of the ketene like intermediate IM1, another rotomer,
represented by IM2 on the potential surface was identified (Fig-3.2). The two rotomers
are connected by a barrier of 372 kJ mol-1 and represented by TS2 (Fig-3.2). The
intermediate IM2 differ from IM1, in the orientation of the ketene moiety (Fig-3.3(d)),
and the transition state TS2 shows an intermediate dihedral angle of 80° (Fig-3.3(c)), thus
92
confirming that the process involves the formation of the rotomer. The intermediate IM2
may undergo a 1,5-proton transfer via the transition state TS3 over a barrier of 390 kJ
mol-1 to form a proton transferred ketene-like intermediate, IM3 (Fig-3.2). However, the
transition state TS3, again encompasses the process of rotation of the terminal C=C bond,
as could be seen from dihedral angle of 80° (Fig-3.3(e)). The proton transferred ketene
IM3, is 150 kJ mol-1 lower in energy than the ketene intermediate IM2 (Fig-3.2). The
stability of the intermediate IM3 is due to the delocalization of charge on to oxygen, as
indicated in Scheme-3.8. The structure of IM3 supports the presence of the resonance
contributing structure as in the structure the length of C=C bond of the ketene moiety is
1.25 Å, clearly providing evidence for the existence of a triple bond and hence the charge
delocalization on to the oxygen atom (Fig-3.3(h)).
Scheme-3.8: Resonance contributing structure of the intermediate IM3
The proton transferred ketene IM3 subsequently undergoes a complex
unimolecular reaction involving the coupling of a proton transfer together with ring
closing process to give the cyclopentadienyl anion via the loss of CO. The initial ion-
dipole complex P1 presents an energy of 139 kJ mol-1 (Fig-3.2) and the structure of P1
(Fig-3.3(k)) indicates a strong π electron interaction which stabilizes the complex. The
reaction occurs over a barrier of 439 kJ mol-1, and the representative transition state to
the process TS5 provides evidence for the complex reaction process (Fig-3.3(i)).
CO
CO
93
The generalized mechanism that could be summarized encompassing all
the important transition states and intermediates from the calculation is given in Scheme-
3.9.
O
C
O
CO
+CO
H HCO
CO
CO
Scheme-3.9: Calculated fragmentation mechanism for phenoxide anion
Surprisingly, a direct transition state TS4, leading to the proton transferred
ketene IM3 and was confirmed by IRC calculation (Fig-3.2). This is rather fascinating, as
both ring opening and proton transfer reactions are coupled together in the same
transition state and the representative transition state TS4 and the processes occur over a
comparable barrier of 403 kJ mol-1 (Fig-3.2). Investigation of the structure of TS4
identifies a intermediate dihedral angle of 78° for C=C of the carbonyl group, which in
this case provides the change in orientation required for the proton transfer to form IM3
(Fig-3.3(g)). The plausible explanation for the coupling of the proton transfer reaction
could be because of the high basicity of the terminal alkene moiety and that the open
ketene structure in the orientation of TS4 is unstable leading to the formation of IM3
immediately after ring opening of the phenoxide anion.
The generalized mechanism encompassing the complex ring cleavage
coupling a proton transfer can be summarized as in Scheme-3.10.
94
+CO
HC
O
CO
C
OOC
O
H
Scheme-3.10: Calculated pathway of phenoxide fragmentation
From these calculations, it is suggestive that the ketene intermediates
dictate the course of the reaction, that the two calculated reaction pathways are equally
competitive. Both the calculated pathways are consistent with the loss of ipso carbon as
CO.
To investigate the involvement of benzene-oxide and oxepin intermediates
in the fragmentation of phenoxide anion, electronic calculations were performed at
B3LYP/6-311++G(d,p) level of theory. The calculated potential energy for the
rearrangement to benzene-oxide and oxepin intermediates is shown in Figure-3.4 with
energies given relative to the phenoxide anion. The electronic energies of the critical
stationary points are listed in Table-3.1 with their molecular structure given in Figure-
3.5. The full Cartesian coordinates of the various stationary points are provided in
Appendix-3.
95
0.0
530.1
408.5
336.5
233.9
470.9
451.2
362.6
507.5
387.7 388.2
151.5
396.1
479.2
337.8
41.8
139.6
TS7
TS11
TS10
IM4IM6
TS13
IM7
TS6
IM8
P1P2
TS12
+
IM5
TS8
TS9
+
Fig-3.4: Potential energy diagram showing the involvement of benzene-oxide and oxepin structures in the fragmentation of phenoxide calculated at B3LYP/6-311++G(d,p) level of theory. All energies given in kJ mol-1.
96
(a) Phenoxide (b) TS6
(c) TS7 (d) IM4
(e) TS8 (f) IM5
97
(g) TS9 (h) IM6
(i) TS10 (j) IM7
(k) TS11 (l) IM8
98
(m) TS12 (n) TS13
(o) P1 (p) P2
Fig-3.5: Structures of the stationary points on the benzene-oxide and oxepin potential energy surface optimized at B3LYP/6-311++G(d,p) level of theory. All lengths, given in angstroms and angles in degrees. All the dihedral angles (Ø) are defined with respect to the plane below, containing the three carbon atoms.
Considering the rearrangement pathway, the phenoxide anion undergoes a
rearrangement to oxepin intermediate IM4 via two different transition states. One of the
transition states, TS7 (Fig-3.5(c)) represents a complex process involving an initial
heterolytic cleavage of C-C bond followed by C-O bond formation to form the seven
membered oxepin intermediate IM4 (Fig-3.4(d)).The transition state TS7 was confirmed by
99
an IRC calculation and it presents a barrier of 470.9 kJ mol-1 (Fig-3.4). The other transition
state TS6 represents an attack of oxygen on to ring at the ortho position and the reaction was
found to be a cyclization process as there was a alternation of double bonds from TS6 (Fig-
3.5(b)) to IM4 (Fig-3.5(d)).The barrier to the process TS6 was found to be 451.2 kJ mol-1
relative to the phenoxide anion (Fig-3.4). The transition state TS6 resembles that of a
benzene-oxide anion as the bond angle of that of a epoxy moiety (C−O−C) is 56° with
dihedral of -56° out of the plane of the benzene ring (Fig-3.5(b)) and is comparable with that
of benzene-oxide where the angle of epoxy moiety is 66° with the corresponding dihedral
angle of -52° (Fig-3.5(j)). The alternation of double bonds in TS6 also matches with that of
the benzene-oxide (IM7) (Fig-3.5(j)).
Following the formation of the oxepin intermediate, a rather surprising one
step ring closure reaction to effect the loss of CO was identified. The transition state TS13 for
this process occurs over a barrier of 508 kJ mol-1 (Fig-3.4), where the loss of CO occurs
perpendicular to the plane of the molecule (Fig-3.5(n)).
The generalised mechanism encompassing all the intermediates to this process
is given in Scheme-3.11.
OC
O
O
O
O
+ CO
Scheme-3.11: Calculated pathway for oxepin fragmentation
100
Now considering the oxepin to benzene-oxide rearrangement, the oxepin
structure IM4 rearranges to IM5, through a ring opening reaction (Fig-3.5). The transition
state TS8 was confirmed by an IRC calculation and it presents a barrier of 408 kJ mol-1 (Fig-
3.4). The new intermediate IM5, is 130 kJ mol-1 lower in energy than the oxepin intermediate
IM4 (Fig-3.4). The stability of the intermediate IM4 is due to the delocalization of the charge
on to the oxygen atom (Scheme-3.12). The structure of IM4 supports the presence of the
resonance contributing structure as in the structure, we could see the simultaneous presence
of triple bond character at the terminal C-C bond and double bond characteristics in the
carbonyl group, thus clearly providing evidence to charge delocalization on to the oxygen
atom (Fig-3.3(h)).
C
HO
C
HO
Scheme-3.12: Resonance contributing structure of the intermediate IM5
Following its formation, the intermediate IM5, undergoes a ring closure
reaction IM6 to form the other oxepin isomer IM6 (Fig-3.4). The transition state TS9 (Fig-
3.5(f)) represents a barrier of 337 kJ mol-1 (Fig-3.4).
The intermediate IM6 then rearranges to the benzene-oxide anion IM7 over a
barrier of 388 kJ mol-1. The transition state to this process is represented by TS10 (Fig-3.4)
and as seen from the transition state structure the process involves a ring closure reaction to
form an epoxy group, with shortening of both the C-C bond distance (1.74 Å) adjacent to the
oxygen atom and the C-O-C bond angle (75°) (Fig-3.5(i)) as compared to the oxepin
intermediate (C-C = 2.35 Å, C-O-C = 108°) (Fig-3.5(h)). The energy of the oxepin
intermediate IM5 is 334 kJ mol-1 and hence the rearrangement occurs over a small barrier of
101
55 kJ mol-1 relative to that of the oxepin intermediate (Fig-3.4). Such rearrangements were
studied for neutral benzene-oxide and oxepin. The two structures are known to exist in
equilibrium in solution, with equilibrium position favouring oxepin at lower temperatures and
benzene-oxide at ambient temperatures.22 Calculation on the neutral system under the same
level of theory found this barrier to rearrangement at 30 kJ mol-1. Calculations were also
conducted for the conversion of the oxepin IM4 to its corresponding benzene-oxide.
However, in this situation the benzene oxide could not be located as stable minima and the
transition state TS10 could be considered as the benzene-oxide structure (Fig-3.4).
The benzene-oxide then undergoes a complex rearrangement to form IM8
over a barrier of 480 kJ mol-1. The transition state to this process is represented as TS11 (Fig-
3.4) and was confirmed by an IRC calculation. On close observation of the structure and after
detailed investigation of the mechanism, the transition state process involves a cross ring
nucleophilic substitution of the negatively charged carbon, thus aiding in the formation of
CHO moiety (Fig-3.5(l)). The transition state structure in fact resembles the intermediate
proposed by Binkley and co-workers (Scheme-3.1(c)).11 The methanolate anion, IM7, is
surprisingly stable, only 42 kJ mol-1, more energetic than phenoxide anion (Scheme-3.13).
C OH
C OH
C OH
C OH
Scheme-3.13: Resonance structures of methanolate anion
Finally, intermediate IM8, then subsequently undergoes a simple 1,2-proton
transfer, via transition state TS12 (Fig-3.5(m)), over a barrier of 396 kJ mol-1 to effect the
formation of cyclopentadienyl anion and the loss of CO (Fig-3.4).
102
The generalized mechanism encompassing all the intermediates to the process
can be hence summarized as in Scheme-3.14.
O CO
O
O
HCH
O
OO
OC O
H
OH
+ CO
CO
Scheme-3.14: Rearrangement of the oxepin to benzene-oxide anion
Interestingly, the intermediate IM8 could also undergo a homolytic cleavage
to effect a loss of CHO.. Bowie and co-workers have observed such loss of CHO. from
phenoxide anions, but only to a minor extent as compared with the CO loss (CHO.:CO
≈1:5).15 The calculated energy of the cyclopentadienyl radical anion and formy radical is 530
kJ mol-1 above the phenoxide anion. This is 50 kJ mol-1 higher in energy than the barrier (s)
for the CO loss (Fig-3.4). The result from the calculation is hence consistent with the
experimental observation. Furthermore, Bowie and co-workers observed the loss of CDO.
103
from 2,4,6 D3 phenoxide anion. The experimental observation here again is consistent with
the mechanism arising from our calculation.
O
CO
O
O
D
CD
O
OOOC O
D
OD
+ DCO
D
D
D
D
D
D
D
D
D
DD
D
D
D
D
D D
D
DD
D
DD
D
D
D
Scheme-3.15: Fragmentation pathway for the loss of CHO.
These calculations have identified a pathway for the loss of CO via
rearrangement to the oxepin structure from phenoxide anion (Scheme-3.11). This calculation
suggest that the transition state TS13 in the direct decarbonylation pathway is a rate
determining step, and that the loss of CO via this pathway could be unfavourable. Our
calculations clearly suggest phenoxide anion rearranges to oxepin and benzene-oxide
intermediates and that the rearrangement pathway eventually effect the loss of CO (Scheme-
104
3.13). The rearrangement pathway is more energetically favourable than the direct
decarbonylation pathway (Fig-3.4).
The other intriguing question would be existence of rearrangement pathways
between ketene intermediates and the oxepin/benzene-oxide intermediates. We might expect
the existence of a transition state between the oxepin intermediate, IM4 (Fig-3.4) and ketene
intermediate, IM1 (Fig-3.2) (Scheme-3.16). Unfortunately, no transition state structure could
be identified between the two intermediates.
CO O
Scheme-3.16: Possible rearrangement between ketene and oxepin intermediates
As discussed earlier, a combined mass spectrometry and computational study
on the rearrangement of perbenzoate anion by Blanksby and co-workers, revealed that a facile
loss of CO2 occurs via an intramolecular epoxidation of the benzene ring, leading to the
formation of benzene-oxide and oxepin as intermediates (Scheme-3.6). Isotopic labelling
studies were also conducted, where the ipso carbon was labeled with 13C carbon and was
subjected to CID. The resulting ion, after the loss of CO2, upon further collisional activation
resulted in an exclusive loss of unlabeled CO.16 As such if these results when interpreted
with the calculated benzene-oxide and oxepin rearrangement from this study suggest that it
would result in the loss of unlabeled CO if benzene-oxide is formed from the perbenzoate
anion i.e. the loss of CO2 occurs via initial nucleophilic substitution at the ortho position of
the perbenzoate anion (Scheme-3.17).
105
13C
OOO
or tho 13C OO
O
13C
OO
O
13C
OCO2
13C
O
13CC
O
H
13C
OH
13C
+ CO
13C
CO
Scheme-3.17: Rearrangement of the labeled perbenzoate anion through initial nucleophilic attack at the ortho position Since, the rearrangement of oxepin to benzene-oxide is the more energetically
favoured pathway, the formation of oxepin from the perbenzoate anion, i.e. the loss of CO2
occurs via initial nucleophilic substitution at the ipso position of the perbenzoate anion would
eventually again lead to the loss of labeled CO (Scheme-3.18).
106
13C
OOO
13CO
OO
13C
OO
O13C
OC
O
O
CO2
13CO
ipso
13C O
H
13C
HO
13CO
C13CO
13C O
+
Scheme-3.18: Rearrangement of the labeled perbenzoate anion through initial nucleophilic attack at the ipso position The calculation does provide compelling evidence to the formation of
benzene-oxide anion i.e. the loss of CO2 occurs via initial nucleophilic substitution at the
ortho position of the perbenzoate anion, which more or less is in accordance with the study.16
107
Table-3.1: Optimized stationary points calculated for the loss of CO from phenoxide anion (Electronic energy zero-point energy, relative energy and imaginary frequency calculated at B3LYP/6-311++G (d, p) level of theory)
Structure
Energy
Hartrees
Zero-point
Energy
Hartrees
Relative energy
kJ mol-1
Phenoxide
-306.99406
0.08945
0
TS1 (-135 cm-1
) -306.83661
0.083076
396.7
IM1 -306.85145
0.08379
359.6
TS2 (-57 cm-1
) -306.84693
0.08386
371.6
IM2 -306.85418
0.08400
352.9
TS3 (-191 cm-1
) -306.83917
0.08311
390.0
IM3 -306.92784
0.08662
166.4
TS4(-133 cm-1
) -306.83413
0.08317
403.4
TS5(-453 cm-1
) -306.82017
0.08265
438.7
P1 -306.93597
0.08452
139.6
TS6(-824 cm-1
) -306.81671
0.08396
451.2
TS7(-225 cm-1
) -306.81033
0.08508
470.9
IM4 -306.85362
0.08712
362.6
IM6 -306.86299
0.08705
337.8
TS10(423 cm-1
) -306.84382
0.08705
388.2
IM7 -306.84514
0.08821
387.7
TS11(310 cm-1
) -306.80762
0.08551
479.2
IM8
-306.97735
0.08867
41.8
TS13(-476 cm-1
) -306.79677
0.08547
507.5
108
TS12-1741cm-1
) -306.83577
0.08204
396.1
Cyclopentadienyl
anion
-193.58082 0.077923
CO -113.34905 0.00504
TS8(-248cm-1
) -306.83085
0.08184
408.5
IM5 -306.90020
0.08467
233.9
TS9(-329cm-1
) -306.86238
0.08593
336.5
3.4 Conclusion
Computational investigations have provided an insight into the
fragmentation of phenoxide anion via the loss of CO and that the fragmentation mechanism
involves ketene like intermediates and transition states and that it truly complements
previously conducted isotopic labeling studies. The calculation also provides evidence for
direct decarbonylation of oxepin intermediate. Our calculations suggest the existence of
rearrangement pathway of phenoxide anion to benzene-oxide and oxepin structures
eventually effecting the loss of CO. The calculations some what provides complementary
and supporting evidence for the previously reported study involving benzene-oxide and
oxepin products from the decarboxylation of perbenzoate anions.
109
References for chapter three
1. Zweig, G.; Sherma, J.; Hanai, J., Phenols and organic acids. CRC Press: Boca Raton,
Fla, 1982. 2. Afghan, B. K.; Chau, S. Y., Analysis of Trace Organics in the Aquatic Environment.
CRC Press: Boca Raton, Fla, 1989. 3. Shahidi, F.; Ho, Chi-Tang., Phenolic compounds in foods and natural health products.
Oxford University Press: Oxford, 2005. 4. Bartsch, H.; Nair, J.; Owen, R. W., J. Biol. Chem. 2002, 383, 915. 5. Hashim, Y. Z.; Eng, M.; Gill, C. I.; McGlynn, H.; Rowland, I. R., Nutr. Rev. 2005, 63,
374. 6. Knust, U.; Erben, G.; Spiengelhalder, B.; Bartsch, H.; Owen, R. W., Rapid Commun.
Mass Spectrom. 2006, 20, 3119. 7. Anderson, G. B.; Gillis, R. G.; Johns, R. B.; Porter, Q. N.; Strachan, M. G., Org. Mass
Spectrom. 1984, 19, 99. 8. Anderson, G. B.; Gillis, R. G.; Johns, R. B.; Porter, Q. N.; Strachan, M. G., Org. Mass
Spectrom. 1984, 19, 583. 9. Bowie, J. H., Mass Spectrom. Rev. 1990, 9, 349. 10. Busch, K. L.; Norstom, A.; Nilsson, C. A.; Bursey, M. M.; Hass, J. R., Environ.
Health Perspec. 1980, 36, 125. 11. Binkley, R. W.; Fletcher, T. W.; Winnik, W., J. Org. Chem. 1992, 57, 5507. 12. Binkley, R. W.; Dillow, G. W.; Fletcher, T. W.; Winnik, W.; Tevesz, M. J. S., Org.
Mass Spectrom. 1994, 29, 491. 13. Flechtner, T. W.; Winnik, B.; Winnik, W.; Tevesz, M. J. S., J. Mass Spectrom. 1996,
31, 377. 14. Eichinger, P. C. H.; Dua, S.; Bowie, J. H., Rapid Commun. Mass Spectrom. 1997, 11,
1996. 15. Eichinger, P. C. H.; Bowie, J. H.; Hayes, R. N., J. Am. Chem. Soc. 1989, 111, 4224. 16. Harman, D. G.; Ramachandran, A.; Gracanin, M.; Blanksby, S. J., J. Org. Chem. 2006,
71, 7996.
110
17. Becke, A. D., J. Chem. Phys. 1993, 98, 1372. 18. Lee, C. T.; Yang, W. T., Parr, R. G., Phys. Rev. B: Condens. Matter 1988, 37, 785. 19. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.;
Cheeseman, J. R.; Montgomery, Jr., J. A.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; and Pople, J. A.; Gaussian 03
(Revision C.02), Gaussian, Inc: Wallingford CT, 2004. 20. Gonzalez, C.; Schlegel, H. B., J. Chem. Phys. 1989, 90, 2154. 21. Gonzalez, C.; Schlegel, H. B., J. Phys. Chem. 1990, 94, 5523. 22. Kassaee, M. Z.; Arshadi, S.; Taheri, N. A., J. Mol. Structure; THEOCHEM 2005, 715,
107.
111
Appendix-1 Table-A_1.1: Tandem mass spectra of [M-H+]- Ions from azo dyes anions para substituted phenyl and sulphonic acid analogues (where phenyl is represented as ph, and Anilinyl as An) Ortho- Ph (m/z) Abundance Loss or fragment
402 100 [M-H]-
385 1 -NH3
374 8 - N2
372 2 -N2H2
338 13 -SO2
322 58 -SO3
310 1 -SO2 -N2
294 4 -SO3 -N2
234 21 -An
221 6 -N2 -ph
Ortho- SO3Hm/z) Abundance Loss or fragment
406 100 [M-H]-
390 9 -NH2
378 5 - N2
376 4 -N2H2
342 ? -SO2
326 50 -SO3
310 4 ?
298 23 -SO3 -N2
296 4 -H2 SO3 - N2
234 6 -An
221 2 -N2 -ph
112
Appendix-2 Table-A_2.1: The Cartesian coordinates for all the stationary points for the fragmentation of 4-amino-3(phenyldiazenyl)benzenesulfonte calculated at B3LYP/6-31+G(d) level as illustrated in Figure-2.16.
Structure
Geometry
4-amino-3(phenyldiazenyl)
Benzenesulfonate
Atom Label X Y Z
C 2.749175 1.540861 0.027289 C 1.698733 2.44557 0.028348 C 2.513212 0.153352 -0.017103 C 0.356253 2.012522 -0.012218 C 1.210566 -0.296502 -0.052588 C 0.107484 0.600014 -0.045459 H 1.008607 -1.362408 -0.08282 S 3.931968 -0.995466 0.008552 O 3.323058 -2.339877 -0.194214 O 4.790477 -0.521124 -1.116073 O 4.535106 -0.782304 1.356817 N -0.666322 2.927536 -0.050497 H -0.462836 3.883088 0.207468 H -1.607353 2.566647 0.07553 N -1.130179 -0.019395 -0.047216 N -2.185176 0.697695 -0.023125 C -3.393792 -0.045469 -0.007159 C -4.581617 0.703357 0.008337 C -3.468405 -1.451568 -0.005012 C -4.711118 -2.080747 0.012682 C -5.894966 -1.330085 0.028388 C -5.823496 0.06627 0.025894 H -2.547554 -2.024192 -0.016897 H -4.759716 -3.167647 0.014808 H -6.860499 -1.830374 0.042521 H -6.734831 0.660167 0.037306 H -4.51108 1.788193 0.004551 H 1.899309 3.516286 0.051928 H 3.774911 1.897838 0.05401
NH2
SO3-
NN
113
IM1
Atom X Y Z
C -1.266711 -0.37664 -0.000192 C -0.10646 0.485148 -0.00014 C -0.29745 1.95695 -0.00001 C -1.67048 2.422849 0.000096 C -2.72312 1.558057 0.000073 C -2.52687 0.131133 -8.7E-05 N 1.066401 -0.1364 -0.00018 N 2.180606 0.574577 -0.00011 C 3.426874 -0.05073 -4.8E-05 C 4.577843 0.758786 -1.6E-05 C 5.843793 0.175346 0.000066 C 5.985295 -1.21679 0.000117 C 4.83668 -2.01761 0.000082 C 3.56339 -1.45042 0.000001 N 0.752463 2.75163 0.000008 S -4.00804 -0.92653 0.000028 O -3.48523 -2.31961 -0.00108 O -4.71764 -0.52073 -1.249 O -4.71638 -0.52225 1.250263 H -1.10842 -1.45042 -0.00033 H 0.461723 3.732985 0.000108 H 2.671666 -2.06653 -1.9E-05 H 4.47043 1.841111 -5.4E-05 H 4.931416 -3.10121 0.000124 H 6.724262 0.814037 0.000092 H 6.973316 -1.66995 0.000185 H -1.83234 3.500276 0.00019 H -3.74369 1.930433 0.00013 H 2.081391 1.609212 -5.8E-05
SO3-
NNN
H H
114
TS2
Atom X Y Z
C -1.41391 0.916089 0.035798 C -0.01961 0.752001 -0.27623 C 0.457102 -0.51705 -0.80167 C -0.47519 -1.59603 -0.89431 C -1.79521 -1.39652 -0.57374 C -2.2782 -0.12919 -0.11096 N 0.794462 1.788933 -0.08191 N 2.089289 1.663589 -0.3193 C 2.902378 0.413128 -0.16678 C 4.172813 0.483663 -0.84807 C 5.297224 -0.15202 -0.34932 C 5.283925 -0.80779 0.896324 C 4.100331 -0.7734 1.640055 C 2.951816 -0.1502 1.15498 N 1.73759 -0.55232 -1.16966 S -4.05408 0.017562 0.275648 O -4.22118 1.41725 0.752275 O -4.26496 -1.03097 1.316028 O -4.71469 -0.28631 -1.02711 H -1.76436 1.875118 0.403931 H 2.098581 -1.47447 -1.42091 H 2.052084 -0.11828 1.764599 H 4.2046 0.99693 -1.80641 H 4.068868 -1.22377 2.630965 H 6.218345 -0.11445 -0.92932 H 6.17762 -1.28846 1.284251 H -0.1236 -2.56269 -1.25037 H -2.50982 -2.20954 -0.6661 H 2.599324 2.481298 0.009087
so3
NNHNH
115
IM2-Cn1
Atom X Y Z
C -1.43986 -0.91528 -0.24549 C -0.07075 0.805951 -0.56898 C 0.507465 -0.48868 -0.71046 C -0.3417 -1.60067 -0.58436 C -1.69688 -1.46798 -0.29066 C -2.25317 -0.19984 -0.09752 N 1.857444 -0.73302 -1.05441 C 2.974388 -0.46579 -0.25517 N 1.761506 2.08538 -1.08258 N 0.533227 2.063494 -0.81057 C 2.890422 0.199486 0.979991 C 4.042552 0.426106 1.734261 C 5.296111 -0.00249 1.287427 C 5.381183 -0.66967 0.05979 C 4.23813 -0.89649 -0.7039 S -4.01554 -0.03864 0.368119 O -4.35014 1.377154 0.051172 O -4.02232 -0.36695 1.822644 O -4.69717 -1.05178 -0.48741 H -1.86769 1.908045 -0.14924 H 1.968608 -1.56843 -1.61642 H 1.924567 0.524791 1.351274 H 4.316963 -1.40055 -1.66593 H 3.952382 0.941616 2.687993 H 6.345073 -1.01357 -0.30999 H 6.187745 0.176924 1.882795 H 0.089785 -2.59453 -0.69932 H -2.33147 -2.34503 -0.20304 H 1.987208 3.079161 -1.25589
so3
NN
HHN
116
IM2-Cn2
Atom X Y Z
C -1.35739 -0.76935 0.402679 C 0.003946 0.554668 -0.68283 C 0.545468 -0.74509 -0.58745 C -0.30093 -1.79818 -0.2065 C -1.6506 -1.57697 0.057515 C -2.18314 -0.28535 -0.03294 N 1.898762 -1.01486 -0.90305 C 3.025522 -0.54388 -0.22278 N 0.656527 2.780193 -0.86846 N 0.856193 1.588048 -1.18227 C 2.94694 0.30448 0.896431 C 4.110475 0.73367 1.535607 C 5.372976 0.327354 1.093172 C 5.453751 -0.52463 -0.01392 C 4.299688 -0.95208 -0.66698 S -3.95668 -0.00063 0.321814 O -4.15104 1.447758 0.03042 O -4.08424 -0.36957 1.760174 O -4.65891 -0.92679 -0.61015 H -1.81514 1.747056 -0.52911 H 2.0406 -1.9017 -1.36915 H 1.978424 0.620514 1.268203 H 4.375507 -1.59862 -1.53979 H 4.022396 1.39145 2.397471 H 6.423891 -0.85435 -0.38016 H 6.273432 0.667395 1.597923 H 0.11795 -2.79835 -0.10844 H -2.29991 -2.40113 0.337887 H -0.13743 2.872911 -0.19078
so3
NHN
NH
117
IM2-Cn3
Atom X Y Z
C -1.41549 0.908048 0.282747 C -0.08258 1.044897 -0.12703 C 0.532341 0.01201 -0.8726 C -0.23442 -1.10412 -1.22377 C -1.58416 -1.19679 -0.87631 C -2.1798 -0.18789 -0.11757 N 1.909161 0.076662 -1.26998 C 2.976852 -0.22691 -0.40908 N 1.369063 2.849986 -0.431 N 0.561003 2.254943 0.311645 C 2.832299 -0.27593 0.98836 C 3.938467 -0.54379 1.796966 C 5.201729 -0.773 1.244876 C 5.346175 -0.72859 -0.14642 C 4.251555 -0.4572 -0.96435 S -3.95837 -0.28704 0.311339 O -4.61632 0.482183 -0.78286 O -4.04182 0.353468 1.65223 O -4.24506 -1.74928 0.293187 H -1.85864 1.680486 0.903945 H 2.060724 -0.25291 -2.21596 H 1.860648 -0.10654 1.439735 H 4.377546 -0.41609 -2.04546 H 3.802533 -0.5748 2.875559 H 6.318675 -0.90497 -0.60132 H 6.05604 -0.98153 1.883491 H 0.24719 -1.9173 -1.7651 H -2.17586 -2.06409 -1.153 H 1.498102 2.3438 -1.33349
so3
NNHN
H
118
TS3
Atom X Y Z
C -1.38058 -0.83745 -0.49749 C 0.005068 0.540779 -0.86816 C 0.607199 -0.70637 -0.70264 C -0.16674 -1.71701 -0.11548 C -1.50713 -1.49112 0.262957 C -2.1208 -0.27011 0.052978 N 1.968444 -0.92927 -1.05207 C 3.067891 -0.49931 -0.30039 N 0.259204 2.743667 -0.58452 N 0.667403 1.736708 -1.11917 C 2.940319 0.329968 0.828325 C 4.075781 0.741505 1.528105 C 5.355011 0.335966 1.137128 C 5.48345 -0.49617 0.019162 C 4.359194 -0.90581 -0.69436 S -3.91785 -0.07611 0.318833 O -4.39352 0.431641 -1.00059 O -4.00238 0.917499 1.425005 O -4.39349 -1.44177 0.673086 H -1.98674 1.415518 -1.20472 H 2.122349 -1.79658 -1.55085 H 1.957943 0.648922 1.158666 H 4.472442 -1.53837 -1.57342 H 3.95053 1.385539 2.395548 H 6.468001 -0.82555 -0.30665 H 6.232713 0.66089 1.689619 H 0.304079 -2.67423 0.098765 H -2.10354 -2.30089 0.673256 H -0.99434 1.927285 0.127951
SO3
NHN
NH
119
IM3
Atom X Y Z
C -1.39365 -0.82687 -0.31779 C 0.045275 0.662404 0.119711 C 0.498068 -0.77874 0.013794 C -0.42203 -1.69792 0.506292 C -1.77108 -1.33395 0.661407 C -2.2749 -0.10699 0.128133 N 1.738354 -1.18167 -0.47069 C 2.994468 -0.64664 -0.17198 N 1.466365 2.463537 -0.28747 N 0.84178 1.569738 -0.73965 C 3.203532 0.19284 0.938565 C 4.478265 0.696364 1.2004 C 5.566378 0.359585 0.3907 C 5.362066 -0.4905 -0.70411 C 4.091339 -0.98031 -0.992 S -4.08543 0.079214 -0.04484 O -4.25524 1.331393 -0.82995 O -4.55287 0.154273 1.369422 O -4.49946 -1.16793 -0.75134 H -1.69976 1.730593 -0.8343 H 1.749214 -2.08866 -0.92107 H 2.375988 0.443373 1.593638 H 3.932329 -1.6133 -1.8629 H 4.617861 1.354192 2.054761 H 6.195795 -0.76066 -1.34849 H 6.556661 0.752182 0.606032 H -0.11737 -2.72818 0.688987 H -2.47904 -2.04812 1.070587 H 0.103756 0.96999 1.2111
SO3
NHN
NH
120
IM4
Atom X Y Z
C -1.61498 1.158878 0.137483 C -0.22906 1.310851 -0.14367 C 0.303455 0.185675 -0.74865 C -0.32863 -1.01331 -1.10234 C -1.68488 -1.09411 -0.80046 C -2.32323 -0.00626 -0.17593 N 1.781839 0.382968 -1.03533 C 2.755714 -0.48307 -0.35424 N 3.116623 3.582561 -0.02066 N 3.034815 4.526604 0.549033 C 2.551536 -0.79411 0.990301 C 3.495375 -1.58472 1.647509 C 4.620533 -2.06414 0.967177 C 4.806871 -1.7482 -0.3805 C 3.871511 -0.94939 -1.04617 S -4.09701 -0.19696 0.242012 O -4.72343 -0.65911 -1.0345 O -4.54102 1.153104 0.692273 O -4.09985 -1.23533 1.318187 H -2.17475 1.961676 0.612523 H 1.978694 0.398453 -2.04216 H 1.660434 -0.43063 1.492564 H 4.01199 -0.69976 -2.09622 H 3.343163 -1.8347 2.693907 H 5.673684 -2.12315 -0.91839 H 5.344829 -2.68789 1.484705 H 0.190158 -1.84728 -1.57729 H -2.25906 -1.98292 -1.04319 H 1.819285 1.374631 -0.68081
so3
H2NN2
121
TS5
Atom X Y Z
C -1.46498 -0.77986 -1.11741 C -0.10218 -1.15247 -1.12304 C 0.554062 -0.91519 0.081887 C 0.03102 -0.37659 1.257901 C -1.31877 -0.0236 1.205876 C -2.05563 -0.22065 0.024644 N 1.957369 -1.38639 -0.12905 C 3.072776 -0.45638 -0.05878 C 2.888911 0.869401 -0.46118 C 3.983002 1.736459 -0.46138 C 5.247642 1.291236 -0.06199 C 5.419281 -0.03714 0.337648 C 4.332092 -0.9145 0.336891 S -3.80074 0.343209 -0.0003 O -4.31032 0.017602 1.366094 O -4.44012 -0.43514 -1.09928 O -3.69504 1.809605 -0.26863 H -2.09535 -0.91979 -1.99227 H 2.1726 -2.24465 0.387636 H 1.900844 1.205945 -0.75755 H 4.463624 -1.94928 0.648139 H 3.841341 2.768419 -0.77146 H 6.39637 -0.39292 0.65489 H 6.092063 1.975691 -0.05825 H 0.617698 -0.22792 2.163799 H -1.82013 0.393738 2.073658 H 1.581664 -1.65671 -1.19236
so3
HN H+ N2
122
so3
H2N
IM5
Atom X Y Z
C -1.61498 1.158878 0.137483 C -0.22906 1.310851 -0.14367 C 0.303455 0.185675 -0.74865 C -0.32863 -1.01331 -1.10234 C -1.68488 -1.09411 -0.80046 C -2.32323 -0.00626 -0.17593 N 1.781839 0.382968 -1.03533 C 2.755714 -0.48307 -0.35424 N 3.116623 3.582561 -0.02066 N 3.034815 4.526604 0.549033 C 2.551536 -0.79411 0.990301 C 3.495375 -1.58472 1.647509 C 4.620533 -2.06414 0.967177 C 4.806871 -1.7482 -0.3805 C 3.871511 -0.94939 -1.04617 S -4.09701 -0.19696 0.242012 O -4.72343 -0.65911 -1.0345 O -4.54102 1.153104 0.692273
IM6
Atom X Y Z
C -1.50204 -0.81894 -1.14742 C -0.15023 -1.24767 -1.23506 C 0.547014 -1.01579 -0.06169 C 0.09841 -0.44948 1.137413 C -1.23614 -0.05199 1.155615 C -2.03078 -0.23299 0.008852 N 1.984572 -1.48541 -0.20168 C 3.06386 -0.49222 -0.10823 C 2.901054 0.73585 -0.75045 C 3.939274 1.666505 -0.69303 C 5.117746 1.376631 0.004287 C 5.262469 0.144694 0.646079 C 4.231424 -0.79872 0.587487 S -3.75493 0.386481 0.063766 O -4.23052 0.024968 1.434343 O -4.4607 -0.32467 -1.04025 O -3.61016 1.859324 -0.14988 H -2.17684 -0.94237 -1.99184 H 2.190499 -2.28153 0.412077 H 1.969799 0.949181 -1.26597 H 4.338525 -1.75973 1.087065 H 3.820081 2.626716 -1.18735 H 6.170964 -0.08503 1.196659 H 5.916583 2.112173 0.05254 H 0.735645 -0.31167 2.011951 H -1.67816 0.387096 2.044552 H 1.858557 -1.85296 -1.18506
SO3-
HN
N2
123
Azo-pro1/Azo-pro-2
Atom X Y Z
C 1.934839 -1.20547 -0.02328 C 2.716391 0.061187 -0.00982 C 2.005069 -1.15581 -0.02633 C 0.608099 -1.16421 -0.04039 C -0.12256 0.027429 -0.04643 C 0.560635 1.256581 -0.04249 H -0.00833 2.181896 -0.0623 N 4.133409 0.098227 -0.04387 H 4.558978 -0.6773 0.45445 H 4.502764 0.97683 0.305301 S -1.95327 -0.00367 0.01175 O -2.35718 1.337537 -0.50085 O -2.26655 -0.22644 1.453961 O -2.32336 -1.14752 -0.87193 H 2.558259 -2.09633 -0.03554 H 0.068532 -2.1064 -0.05976
Azo-pro1
Atom X Y Z
N -2.88199 -0.32815 -0.000016 N -2.01717 -0.48214 -0.000007 C -0.58992 -0.19137 0.000023 C -0.09765 1.119118 0.000014 C 0.268718 -1.29078 0.000007 C 1.28147 1.320279 -0.000006 H -0.79173 1.954338 0.000026 C 1.649442 -1.07831 -0.000004 H -0.15204 -2.29208 0.000018 C 2.15511 0.224649 -0.000007 H 1.678265 2.332144 -0.000001 H 2.327266 -1.92748 -0.000017 H 3.229312 0.389446 -0.000027
NH2
SO3-
NN
124
NH
Azo-pro2
Atom X Y Z
C -0.000012 -1.40007 0.000005 C -1.228195 -0.77313 -0.00013 C 1.228203 -0.77311 0.000124 C -1.215812 0.63329 0.00011 H -2.164547 -1.32522 -8.20E-05 C 1.215825 0.633255 -0.00012 H 2.164525 -1.32526 0.000085 C -0.000009 1.326232 0.000004 H -2.156816 1.179302 0.000137 H 2.156795 1.179331 -0.00013 H 0.000042 2.413073 0.000002
Tau-pro
Atom X Y Z
N -2.35783 -0.13736 -0.00037 C -1.02058 -0.02988 0.000541 C -0.30317 1.214242 -0.00044 C 1.081736 1.236063 0.000194 C 1.811138 0.033046 -2.00E-06 C 1.135356 -1.20072 -0.00031 C -0.2488 -1.23958 0.000307 H -0.7927 -2.17938 0.001005 H -0.86957 2.143507 0.0002 H 1.704161 -2.12694 -0.00053 H 1.609443 2.186585 0.001076 H 2.897506 0.058742 -0.00083 H -2.77814 0.799915 -0.00011
125
Tau-Pro
Atom X Y Z
C -0.49202 -1.0748 -0.0002 C -1.963 0.971687 0.000087 C -2.59081 -0.41762 -7.90E-05 C -1.65596 -1.54373 0.00036 C -0.31567 -1.36586 0.000343 C 0.277026 -0.03436 0.000019 N -2.68288 2.020334 0.00052 N -3.87781 -0.52063 -0.00063 S 2.098429 0.043367 -5.90E-05 O 2.428298 1.491417 -0.00037 O 2.454362 -0.68909 -1.24975 O 2.454415 -0.6886 1.249915 H -0.04188 2.061569 -0.00038 H -4.13502 -1.51486 -0.00058 H -2.08904 -2.54347 0.000523 H 0.361836 -2.21437 0.00057
Pro
Atom X Y Z
S 3.883004 -0.30459 -0.07761 C 2.115594 -0.14733 0.052195 C 1.249392 0.637403 0.822068 C -0.10139 0.309059 0.929539 C -0.61411 -0.80329 0.241617 C 0.255032 -1.58618 -0.52912 C 1.61369 -1.26554 -0.61333 H 1.646371 1.496034 1.356081 H -0.75944 0.898951 1.562521 H -0.13674 -2.44735 -1.06953 O 4.487431 -0.80846 -0.86529 O 3.864654 1.620423 -0.78023 O 4.34022 0.381258 1.340143 H 2.297724 -1.8698 -1.20147 N -1.97711 -1.18793 0.371817 C -3.10264 -0.40972 0.122614 H -2.13905 -2.18582 0.346957 C -4.38006 -0.98539 0.30471 C -5.53826 -0.25032 0.06446 C -5.4649 1.082751 -0.35651 C -4.20268 1.656315 -0.54018 C -3.03333 0.930347 -0.31034 H -4.4522 -2.01786 0.643787 H -6.50688 -0.72367 0.212857 H -6.36882 1.658094 -0.5385 H -4.11913 2.687237 -0.87788 H -2.06665 1.391719 -0.47903
SO3-
NHN
SO3-
HN
126
N2
Atom X Y Z
N 0 0 -0.00256 N 0 0 1.102563
127
(a) 4-amino-3(phenyldiazenyl)benzenesulfonate (b) TS1
(c) IM1 (d) TS2
128
(e) IM2-Cn1 (f) IM2-Cn2
(f) IM2-Cn3 (g) TS3
129
(h) IM3 (i) TS4
K
(j) IM6 (k) Pro
130
(l) Tau-Pro (m) Azo-Pro1
(n) Azo-Pro2 (Benzene Radical) (o) nitrogen
Fig-A_2.1:Structures of the stationary points on the 4-amino-3(phenyldiazenyl)benzenesulfonate potential energy surface optimized at B3LYP/6-311++G(d,p) level of theory. All lengths given in angstroms and angles in degrees.
131
Table-A_2.2: Optimized stationary points calculated for the loss of N2 from 4-hydroxy-3-(phenyldiazenyl)benzenesulfonate Anion (Electronic energy zero-point energy, relative energy and imaginary frequency calculated at B3LYP/6-31+G(d) level of theory)
Structure
Energy
Hartrees
Zero-point Energy
Hartrees
Relative energy
kJ mol-1
4-hydroxy-3
(phenyldiazenyl)
benzenesulfonate
-1271.31579
0.19772
0.0
Hyd-TS1(-1337cm-1
) -1271.30811
0.19335
8.7
Hyd-IM1 -1271.31496
0.19782
2.4
Hyd-TS2(-287cm-1
) -1271.23567
0.19562
204.9
Hyd-IM2-Cn1 -1271.28081
0.19677
89.3
Hyd-IM2-Cn2 -1271.27927
0.19638
92.4
Hyd-IM2-Cn3 -1271.27686
0.19658
99.2
Hyd-TS3 (-655cm-1
) -1271.16294 0.19015
381.3
Hyd-IM3 -1271.16655
0.19250
378.1
Hyd-IM5 -1271.36196
0.19333
-132.7
Hyd-TS4(-509cm-1
) -1271.18053
0.18987
334.5
Hyd-Pro -1271.35995
0.19297
-128.4
Hyd-IM-New -1271.26244
0.18976
119.2
Hyd-Pro2 -1271.23115
0.18763
195.7
132
Table-A_2.3: Optimized stationary points calculated for the loss of N2 from (4-(4-sulfonatophenylamino) benzene-1-sulfonic acid) (Electronic energy zero-point energy, relative energy and imaginary frequency calculated at B3LYP/6-31+G(d) level of theory)
Structure
Energy
Hartrees
Zero-point Energy
Hartrees
Relative energy
kJ mol-1
(4-(4-sulfonato
phenyl amino)
benzene-1-sulfonic
acid)
-1874.69247
0.21196
0.0
DI-IM1 -1874.67982
0.21233
34.2
DI-IM2Cn2 -1874.66206
0.21192
79.7
DI-IM2Cn3 -1874.66017
0.21151
83.6
DI-IM6
-1765.095745
0.2022
-
DI-Pro -1765.21296
0.20242
-
133
Table-A_2.4: The Cartesian coordinates for all the stationary points for the fragmentation of 4-amino-3(phenyldiazenyl)benzenesulfonte calculated at B3LYP/6-31+G(d) level as illustrated in Figure-2.17.
Structure
Geometry
4-hydroxy-
3(phenyldiazenyl)
Benzenesulfonate
Atom X Y Z
C 2.705722 1.559882 -0.00495 C 1.620101 2.430033 0.000222 C 2.524348 0.163992 -0.01389 C 0.312921 1.928757 -0.00139 C 1.241411 -0.34594 -0.01738 C 0.112411 0.512938 -0.01121 H 1.085107 -1.42007 -0.02854 S 3.987846 -0.93131 0.004487 O 3.422991 -2.29879 -0.16807 O 4.805988 -0.4421 -1.14239 O 4.601816 -0.67437 1.339026 N -1.12198 -0.11463 -0.01297 N -2.15916 0.628609 -0.00371 C -3.3985 -0.05622 -0.00176 C -4.55142 0.744413 0.005648 C -3.52777 -1.4575 -0.00517 C -4.79561 -2.03413 -0.00107 C -5.94642 -1.23372 0.006354 C -5.81814 0.15839 0.009586 H -2.63139 -2.06778 -0.01056 H -4.88981 -3.11777 -0.00335 H -6.93194 -1.69323 0.009822 H -6.70405 0.789136 0.015447 H -4.43597 1.82519 0.00848 H 1.758235 3.507942 0.005046 H 3.71795 1.954226 -0.008 O -0.7218 2.797103 0.004333 H -1.55197 2.245355 0.003473
OH
SO3-
NN
134
Hyd-TS1
Atom X Y Z
C -2.63478 1.569959 0.000518 C -1.51927 2.385275 0.000719 C -2.53416 0.150744 -0.00042 C -0.22167 1.816546 0.000147 C -1.29623 -0.43818 -0.00102 C -0.11765 0.366658 -0.00067 H -1.2033 -1.51995 -0.00181 S -4.06971 -0.83489 0.000041 O -3.60269 -2.24877 -0.00615 O -4.75649 -0.40718 1.253338 O -4.76289 -0.39825 -1.24664 N 1.082917 -0.26722 -0.0009 N 2.125129 0.505772 -0.00063 C 3.401691 -0.07494 -0.00031 C 4.504774 0.795911 -0.0007 C 3.612923 -1.46569 0.00051 C 4.913704 -1.96466 0.000952 C 6.015117 -1.09881 0.000573 C 5.801813 0.28357 -0.00026 H 2.75517 -2.129 0.000853 H 5.070276 -3.04097 0.001637 H 7.026346 -1.4979 0.00095 H 6.647693 0.966988 -0.00057 H 4.331831 1.869107 -0.00134 H -1.60345 3.46861 0.001319 H -3.62834 2.01 0.00087 O 0.865922 2.543169 0.000464 H 1.754394 1.691361 -0.00018
SO3
ONN
H
135
Hyd-IM1
Atom X Y Z
C -1.37417 -0.89325 -0.18345 C -0.00174 0.649238 -0.4561 C 0.471214 -0.68793 -0.58989 C -0.43178 -1.7498 -0.45922 C -1.77492 -1.48394 -0.21397 C -2.25297 -0.16231 -0.07007 N 0.841359 1.717313 -0.59611 N 2.06368 1.403764 -0.8509 C 2.792939 -0.00042 -0.31174 C 4.067365 -0.17168 -0.9816 C 5.256025 -0.22594 -0.28151 C 5.298214 -0.1328 1.124975 C 4.084365 -0.00372 1.803673 C 2.866244 0.040163 1.128938 S -4.02987 0.110473 0.267331 O -4.15422 1.589658 0.381222 O -4.25987 -0.63836 1.535511 O -4.70326 -0.48616 -0.92107 H -1.72637 1.913758 -0.06891 H 1.938994 0.118129 1.690576 H 4.052647 -0.26316 -2.06489 H 4.072763 0.047553 2.891129 H 6.181624 -0.35364 -0.84092 H 6.241953 -0.17625 1.660626 H -0.06119 -2.76605 -0.55964 H -2.48195 -2.30346 -0.12149 H 2.694041 2.211064 -0.83569 O 1.770526 -0.9436 -0.86557
SO3-
ONN
H
136
Hyd-IM2Cn1
Atom X Y Z
C -1.504 0.986694 0.438193 C -0.16242 1.311497 0.173893 C 0.592235 0.449273 -0.64764 C 0.003386 -0.68369 -1.20787 C -1.34126 -0.9665 -0.96717 C -2.10085 -0.12753 -0.14474 C 2.924766 -0.02803 -0.33669 N 1.208465 3.198251 0.312002 N 0.339755 2.472412 0.843462 C 2.711026 -0.86195 0.765587 C 3.792266 -1.56295 1.308186 C 5.074456 -1.43831 0.767378 C 5.273189 -0.59719 -0.33357 C 4.204757 0.106457 -0.88842 S -3.87493 -0.49325 0.133188 O -4.53488 0.05379 -1.08593 O -4.19982 0.23019 1.392569 O -3.91156 -1.97974 0.233728 H -2.07981 1.618093 1.107781 H 1.719029 -0.96093 1.192951 H 4.340988 0.762532 -1.74335 H 3.62256 -2.20915 2.166043 H 6.265178 -0.48868 -0.76611 H 5.908083 -1.98739 1.197379 H 0.612096 -1.33862 -1.8264 H -1.80724 -1.84847 -1.39593 H 1.476911 2.848205 -0.63071 O 1.933544 0.730142 -0.92583
so3
NN
HO
137
Hyd-IM2-Cn2
Atom X Y Z
C -1.48561 1.043111 0.181789 C -0.1149 1.210167 -0.08576 C 0.563127 0.194891 -0.80239 C -0.13454 -0.9317 -1.23128 C -1.49011 -1.09063 -0.92881 C -2.16975 -0.10423 -0.21104 C 2.90486 -0.14777 -0.43776 N 1.666532 2.54918 0.424324 N 0.416421 2.444564 0.370939 C 2.716664 -0.80062 0.784835 C 3.830192 -1.27241 1.486762 C 5.122569 -1.10295 0.98415 C 5.296173 -0.44696 -0.24088 C 4.196038 0.029328 -0.95184 S -3.92859 -0.34148 0.241689 O -4.4762 1.041741 0.301386 O -3.85334 -1.03288 1.56036 O -4.46724 -1.18469 -0.86267 H -2.01393 1.836853 0.700686 H 1.716788 -0.93485 1.183674 H 4.313239 0.545316 -1.90038 H 3.677021 -1.77641 2.438347 H 6.295518 -0.30412 -0.64652 H 5.981829 -1.47399 1.537109 H 0.401471 -1.68039 -1.80931 H -2.03651 -1.96666 -1.26525 H 1.848888 3.507982 0.765531 O 1.882281 0.33485 -1.21463
so3
NO
NH
138
Hyd-IM2-Cn3
Atom X Y Z
C -1.35412 -0.94011 -0.15633 C 0.006722 0.93115 -0.50957 C 0.599332 -0.28156 -0.90276 C -0.14534 -1.46062 -0.91192 C -1.49052 -1.43864 -0.54236 C -2.09761 -0.235 -0.16436 C 2.9478 -0.34449 -0.43228 N 0.557188 3.079502 0.181792 N 0.8148 2.110161 -0.5619 C 2.771276 -0.51861 0.944757 C 3.893859 -0.55724 1.778083 C 5.182392 -0.42872 1.254909 C 5.34396 -0.25767 -0.12558 C 4.235495 -0.21479 -0.96906 S -3.86477 -0.21409 0.320757 O -4.15252 1.229741 0.550138 O -3.89036 -1.05762 1.549046 O -4.5639 -0.81496 -0.84867 H -1.87354 1.863768 0.086423 H 1.774367 -0.62192 1.36023 H 4.341782 -0.07436 -2.04067 H 3.750218 -0.68909 2.848006 H 6.340173 -0.15133 -0.54924 H 6.048373 -0.45783 1.911188 H 0.342296 -2.3837 -1.21381 H -2.08121 -2.34973 -0.55673 H -0.24859 2.873998 0.818937 O 1.916655 -0.32161 -1.34012
so3
NNO
H
139
Hyd-IM3
Atom X Y Z
C -1.73204 -1.13467 -0.21334 C -0.36708 1.500774 0.270544 C 0.65633 0.446223 -0.03268 C 0.26541 -0.83895 0.272406 C -1.11947 -1.09726 0.436244 C -2.1158 -0.14522 0.08214 C 3.011078 0.08243 -0.21909 N 0.278882 3.657262 0.61553 N 0.053701 2.846533 -0.21956 C 3.352498 -0.36543 1.060093 C 4.542745 -1.07374 1.236221 C 5.387259 -1.328 0.14957 C 5.035352 -0.86562 -1.12173 C 3.844808 -0.15893 -1.31174 S -3.84584 -0.71769 -0.10183 O -4.51415 0.385371 -0.84394 O -4.29853 -0.89023 1.307967 O -3.71557 -1.99685 -0.85732 H -2.39999 1.873386 -0.64274 H 2.695538 -0.15604 1.898658 H 3.551237 0.210408 -2.28962 H 4.813166 -1.42199 2.230071 H 5.685447 -1.05656 -1.97203 H 6.312286 -1.88005 0.294537 H 0.969371 -1.66675 0.273069 H -1.43986 -2.1058 0.679405 H -0.42235 1.526239 1.412327 O 1.887494 0.862708 -0.44147
SO3
NO
NH
140
Hyd-Pro
Atom X Y Z
S -3.76879 -0.33994 -0.01268 C -2.02758 -0.22384 0.022057 C -1.38924 -0.60602 -1.16087 C -0.03977 -0.97266 -1.14835 C 0.660186 -0.95254 0.056788 C 0.032625 -0.59066 1.248819 C -1.31564 -0.22374 1.225462 H -1.96221 -0.62503 -2.08306 H 0.470419 -1.27808 -2.05856 H 0.596523 -0.60376 2.178342 O -4.3011 -0.04076 1.326827 O -3.65478 1.811874 -0.22867 O -4.36887 -0.40116 -1.15856 H -1.83271 0.050137 2.140255 C 3.004815 -0.45226 0.020727 C 4.309262 -0.9598 0.119897 C 5.398941 -0.09261 0.063142 C 5.2046 1.28558 -0.09182 C 3.901862 1.780679 -0.19063 C 2.797491 0.924289 -0.1364 H 4.44283 -2.03126 0.239921 H 6.406191 -0.49627 0.141437 H 6.055511 1.960694 -0.13458 H 3.732648 2.848212 -0.31193 H 1.789758 1.317469 -0.21426 O 1.996781 -1.37989 0.076944
SO3-
O
141
Hyd-TS3
Atom X Y Z
C -1.726605 -1.1425 -0.201079 C -0.322947 1.480859 0.021144 C 0.654355 0.434858 -0.293828 C 0.255288 -0.88197 -0.125888 C -1.109013 -1.17471 0.038159 C -2.100534 -0.17233 -0.039408 C 3.020761 0.087467 -0.260778 N 0.308415 3.307268 0.909642 N 0.082673 2.867915 -0.204693 C 3.208685 -0.38582 1.041128 C 4.382846 -1.07508 1.349807 C 5.363997 -1.28396 0.37402 C 5.165202 -0.79494 -0.920302 C 3.992027 -0.10806 -1.243761 S -3.865822 -0.66648 -0.010989 O -4.583854 0.535999 -0.512765 O -4.104559 -0.98547 1.424705 O -3.910313 -1.8511 -0.914213 H -2.461589 1.924577 -0.361049 H 2.448065 -0.20964 1.795482 H 3.816952 0.281473 -2.242075 H 4.533059 -1.44263 2.361911 H 5.922299 -0.94977 -1.68518 H 6.276062 -1.82042 0.622556 H 0.977328 -1.68955 -0.208421 H -1.42634 -2.20848 0.134323 H -0.209086 1.566262 1.272603 O 1.91553 0.847134 -0.608259
SO3
NO
NH
142
Hyd-IM5
Atom X Y Z
C -0.90928 0.731762 0.061358 C 0.398906 1.110223 -0.25439 C 1.236045 0.196679 -0.89367 C 0.784879 -1.07699 -1.23709 C -0.52512 -1.44588 -0.91727 C -1.3716 -0.54698 -0.26226 C 3.572713 0.406477 -0.39884 N -5.42848 2.947255 0.354312 N -6.30709 2.303277 0.169751 C 3.445264 -0.17711 0.868289 C 4.579953 -0.31823 1.673739 C 5.834466 0.112578 1.235141 C 5.948949 0.694277 -0.03363 C 4.828265 0.842325 -0.84892 S -3.05783 -1.06482 0.224708 O -3.85091 0.197618 0.186396 O -2.87141 -1.62531 1.594474 O -3.44099 -2.07322 -0.80353 H -1.58684 1.427227 0.547457 H 2.475426 -0.51423 1.217463 H 4.900281 1.290998 -1.83571 H 4.47267 -0.77171 2.656513 H 6.91769 1.035757 -0.39214 H 6.70941 -0.00188 1.869958 H 1.45362 -1.76157 -1.75295 H -0.90749 -2.4266 -1.18389 H 0.771083 2.103603 -0.01627 O 2.529262 0.591789 -1.26845
SO3-
O
N2
143
Hyd-TS4
Atom X Y Z
C -1.49319 0.9831 0.485291 C -0.13221 1.252553 0.251238 C 0.44063 0.440017 -0.67902 C -0.12547 -0.59843 -1.40437 C -1.46956 -0.85205 -1.12012 C -2.14742 -0.06865 -0.17179 C 2.892492 -0.06993 -0.30445 N 1.907884 3.109701 -0.20508 N 0.948577 3.164001 0.423794 C 2.854007 -0.17327 1.083229 C 3.828251 -0.95197 1.712698 C 4.81322 -1.60279 0.962 C 4.827439 -1.47913 -0.43083 C 3.858343 -0.70645 -1.07708 S -3.88602 -0.48882 0.23214 O -4.43346 -1.03275 -1.04597 O -4.49209 0.800467 0.668678 O -3.75809 -1.5059 1.317614 H -2.07068 1.587763 1.181942 H 2.066285 0.327459 1.638052 H 3.841196 -0.59672 -2.15702 H 3.8117 -1.0511 2.794705 H 5.587982 -1.9869 -1.01826 H 5.565802 -2.20744 1.461395 H 0.431226 -1.17279 -2.14218 H -2.01068 -1.63744 -1.63825 H 2.064182 1.769989 -0.76269 O 1.935492 0.717475 -0.99579
SO3
O
NN
H
144
Hyd-IM-New
Atom X Y Z
C -3.56215 -0.91717 0.023938 C 3.992283 -2.08061 -0.58629 C 3.346984 -3.07081 -1.0076 C 1.95718 -3.16803 -0.92602 C 1.380684 -2.03285 -0.31877 C 2.154794 -0.94856 0.137538 C -2.87379 0.2434 -0.68922 N 2.393509 3.834396 -1.17836 N 1.712422 4.410718 -0.52679 C -4.12358 0.107325 -1.32054 C -5.21793 -0.3947 -0.61568 C -5.09012 -0.76971 0.727356 C -3.84441 -0.63244 1.350765 C -2.73774 -0.13187 0.66041 S 1.313318 0.488308 0.904295 O 0.542732 1.103578 -0.2321 O 2.410806 1.352189 1.400505 O 0.430678 -0.09907 1.946956 H 4.14111 -0.07685 0.385867 H -4.21194 0.402577 -2.36303 H -1.77509 -0.03526 1.158158 H -6.1779 -0.49272 -1.12024 H -3.72314 -0.91898 2.393695 H -5.94393 -1.16066 1.276259 H 1.350964 -3.99978 -1.27294 H 0.30247 -1.99365 -0.18944 H -1.01034 0.82115 -0.90559 O -1.85245 0.730994 -1.42921
SO3OH
N2
145
Hyd-pro2 (product-1)
Atom X Y Z
C 0.972065 -1.36174 -0.000091 C 2.346222 1.217444 0.00004 C 3.086356 0.201938 0.000043 C 2.554906 -1.092422 0.00002 C 1.144284 -1.101949 -0.000094 C 0.378856 0.080231 -0.000151 S -1.462762 -0.038818 0.000012 O -1.767627 -0.789978 -1.250182 O -1.91632 1.380347 -0.001523 O -1.767527 -0.787207 1.251895 H 0.370496 2.261981 -0.000174 H 3.130419 -2.014799 0.00006 H 0.618935 -2.05329 -0.000197
SO3
146
Hyd-pro2 (product-2)
Atom X Y Z
C -0.939798 -0.023554 0.000232 C -0.263735 1.201313 0.000117 C 1.134209 1.220458 0.000055 C 1.859905 0.027024 -0.000147 C 1.172265 -1.192406 -0.000049 C -0.222087 -1.224634 0.000194 H -0.8247 2.134767 -0.000044 H -0.76704 -2.163978 0.000371 H 1.652712 2.175981 -0.000073 H 1.725387 -2.128273 -0.00016 H 2.946061 0.045231 -0.000304 H -2.697608 0.777793 0.000421 O -2.30992 -0.111342 -0.000327
OH
147
Table-A_2.5: The Cartesian coordinates for all the stationary points for the fragmentation of (4-(4-sulfonatophenylamino) benzene-1-sulfonic acid) calculated at B3LYP/6-31+G(d) level as illustrated in Figure-2.17.
Structure Geometry
(4-(4-sulfonato phenyl amino) benzene-1-
sulfonic acid)
Atom X Y Z
C 4.669307 1.321165 0.063962 C 3.737058 2.348685 0.062299 C 4.257727 -0.01986 -0.00464 C 2.351925 2.09081 -0.00461 C 2.903104 -0.29916 -0.06137 C 1.924618 0.726609 -0.05624 H 2.566496 -1.33012 -0.10463 S 5.525384 -1.33306 0.011835 O 4.764296 -2.60213 -0.16629 O 6.425038 -0.98413 -1.1303 O 6.183174 -1.18886 1.346642 N 1.459083 3.144802 -0.06013 H 1.776516 4.030039 0.312438 H 0.483906 2.891166 0.081424 N 0.601821 0.266488 -0.07262 N -0.3297 1.130684 -0.04972 C -1.65251 0.621522 -0.04086 C -2.67373 1.584582 -0.02601 C -1.99942 -0.74467 -0.04606 C -3.33963 -1.1191 -0.03481 C -4.35651 -0.15046 -0.01761 C -4.01664 1.203576 -0.01421 H -1.20978 -1.48893 -0.06008 H -3.61418 -2.17018 -0.04476 H -4.81376 1.940496 -0.00859 H -2.39513 2.636479 -0.02763 H 4.06874 3.386719 0.099985 H 5.730974 1.54674 0.111888 S -6.11086 -0.66351 0.028284 O -6.27673 -1.27792 1.379146 O -6.2412 -1.63549 -1.09684 O -6.87664 0.604355 -0.16282
NH2
SO3
NN
SO3
148
DI-IM1
Atom X Y Z
C 4.646263 1.36658 0.004679 C 3.703247 2.35382 0.005436 C 4.279206 -0.02005 0.001567 C 2.284227 2.063159 0.003242 C 2.959679 -0.36399 -0.00078 C 1.918533 0.633446 -0.00021 H 2.666023 -1.40906 -0.00326 S 5.619268 -1.25118 0.001014 O 4.935857 -2.57471 -0.00323 O 6.386316 -0.9437 -1.24543 O 6.382048 -0.94951 1.251468 N 1.339695 2.988467 0.003903 H 1.754864 3.923957 0.006174 H -0.10293 2.012512 -0.00053 N 0.666258 0.158448 -0.00357 N -0.3375 0.998098 -0.00335 C -1.67539 0.569451 -0.00731 C -2.67205 1.558637 -0.00955 C -2.04141 -0.78693 -0.01206 C -3.39149 -1.133 -0.01811 C -4.38953 -0.14906 -0.01876 C -4.01978 1.197703 -0.01459 H -1.26724 -1.54676 -0.014 H -3.68226 -2.17951 -0.03052 H -4.80037 1.952074 -0.02393 H -2.3846 2.608683 -0.00967 H 3.997328 3.403678 0.007789 H 5.703948 1.616056 0.006384 S -6.15358 -0.62539 0.006727 O -6.36854 -1.17584 1.378305 O -6.27795 -1.64413 -1.07715 O -6.88574 0.64912 -0.25928
SO3
NHN
HN
SO3
149
DI-IM2Cn3
Atom X Y Z
C -3.00643 -0.68825 0.56789 C -1.68901 -0.26363 0.859575 C -1.22066 0.976866 0.331933 C -2.14982 1.752318 -0.39811 C -3.45572 1.338517 -0.62352 C -3.89588 0.095544 -0.14897 N 0.046232 1.537661 0.527231 C 1.32743 0.981197 0.315984 N 0.046507 -0.72678 2.269323 N -1.02508 -1.13849 1.751567 C 1.551677 -0.28065 -0.25013 C 2.859492 -0.73115 -0.46828 C 3.957839 0.061038 -0.13315 C 3.735698 1.321401 0.433803 C 2.438972 1.772966 0.660843 S -5.61422 -0.43431 -0.46984 O -5.75546 -1.72601 0.261752 O -5.69338 -0.55406 -1.95635 O -6.4412 0.68165 0.082209 H -3.33282 -1.64306 0.967254 H 0.042165 2.537687 0.368686 H 0.709716 -0.90401 -0.53517 H 2.273521 2.744578 1.12639 H 3.034904 -1.71202 -0.90017 H 4.588782 1.933839 0.711423 H -1.81025 2.701588 -0.81274 H -4.13915 1.967949 -1.18652 H 0.365912 -1.48565 2.893384 S 5.663916 -0.48871 -0.4798 O 5.56746 -1.974 -0.59921 O 6.028477 0.199578 -1.7563 O 6.453716 -0.01421 0.697604
so3
NNHN
SO3
H
150
DI-IM2Cn2
Atom X Y Z
C -2.96327 -0.66037 -0.52904 C -1.65585 0.265274 -0.87207 C -1.17565 -1.00729 -0.48599 C -2.03834 -1.83652 0.257006 C -3.33451 -1.44287 0.575758 C -3.80598 -0.18469 0.182355 N 0.084702 -1.49742 -0.8679 C 1.360323 -0.95333 -0.56066 N -0.92049 2.296431 -1.73002 N -0.8436 1.0501 -1.74446 C 1.559479 0.164997 0.258665 C 2.858258 0.593815 0.559777 C 3.972948 -0.0831 0.06409 C 3.775121 -1.19338 -0.76351 C 2.486919 -1.61735 -1.07993 S -5.53717 0.290531 0.530796 O -5.60675 1.73227 0.153212 O -5.70184 0.020812 1.989316 O -6.34599 -0.61226 -0.34142 H -3.36754 1.608329 -0.87353 H 0.106315 -2.50987 -0.87618 H 0.707812 0.694286 0.675483 H 2.340768 -2.4701 -1.7427 H 3.013875 1.462375 1.192797 H 4.63894 -1.71211 -1.16957 H -1.66814 -2.80504 0.590797 H -3.98822 -2.10334 1.138141 H -1.568 2.630987 -0.97592 S 5.668222 0.401875 0.538124 O 5.537835 1.801013 1.042192 O 6.461748 0.26952 -0.72161 O 6.055777 -0.58803 1.590275
SO3
NHN
NH
SO3
151
DI-IM6
Atom X Y Z
C 3.469271 -0.9552 -1018229 C 2.178332 1.543745 -1.096197 C 1.345813 1.11286 -0.07688 C 1.622305 0.217073 0.961449 C 2.909698 -0.31926 0.98335 C 3.835175 0.061293 -0.003517 N 0.014759 1.858438 -0.103928 C -1.28511 1.165657 -0.035815 C -1.53889 0.069977 -0.859321 C -2.80887 -0.5139 -0.833275 C -3.80728 -0.01354 0.009548 C -3.52805 1.067283 0.84863 C -2.26443 1.661244 0.825046 S 5.512755 -0.6771 0.05403 O 5.820928 -0.79457 1.515124 O 6.39244 0.286725 -0.673879 O 5.371446 -2.00021 -0.630429 H 4.232537 1.209047 -1.751501 H 0.026669 2.589339 0.614969 H -0.75212 -0.31819 -1.499815 H -2.04591 2.507802 1.475672 H -3.03355 -1.37213 -1.458958 H -4.30107 1.428883 1.519623 H 0.885349 -0.06667 1.713279 H 3.213688 -1.01246 1.761432 H 0.17032 2.348468 -1.014966 S -5.50185 -0.70937 -0.02915 O -5.98905 -0.55473 1.372207 O -6.21061 0.15798 -1.01575 O -5.31534 -2.11837 -0.474654
SO3
H2N
SO3
152
DI-Pro
Atom X Y Z
S -5.66495 -0.59167 -0.02587 C 3.942605 0.011465 -0.01467 C 2.885022 -0.79225 -0.43999 C 1.566174 -0.32066 -0.43468 C 1.280227 0.978931 0.015942 C 2.355479 1.78215 0.453065 C 3.663831 1.308947 0.429318 H 3.106324 -1.79381 -0.79691 H 0.769082 -0.95372 -0.81025 H 2.150382 2.790504 0.813731 O 6.410517 0.431299 -0.82212 O 6.064084 -0.62719 1.41437 O 5.589961 -1.93566 -0.67244 H 4.479897 1.945745 0.75967 N -6E-06 1.553657 0.000032 C -1.28022 0.978884 -0.01597 H -2.7E-05 2.564002 0.000111 C -2.35549 1.782121 -0.45304 C -3.66382 1.308865 -0.4294 C -3.94256 0.011307 0.014398 C -2.88497 -0.79242 0.439645 C -1.56613 -0.32079 0.434436 H -2.15041 2.79051 -0.81361 H -4.47986 1.94565 -0.75984 H -3.10625 -1.79409 0.796291 H -0.76902 -0.95389 0.809902 S -5.66497 -0.59164 0.025966 O -6.06583 -0.62289 -1.41389 O -6.40946 0.429079 0.826098 O -5.58937 -1.93751 0.66857
SO3
HN
SO3
153
Appendix-3 Table-A_3.1: The Cartesian coordinates for all the stationary points for the fragmentation of phenoxide anion calculated at B3LYP/6-31+G(d) level as illustrated in Figure-3.3. Structure
Geometry
Phenoxide
Atom X Y Z
C 0.287528 -1.21168 -5E-06 C -1.10006 -1.20007 0.000007 C -1.82771 0.000001 -1E-06 C -1.10016 1.199922 0.000007 C 0.287595 1.211748 -4E-06 C 1.077275 0.00015 -6.1E-05 O 2.347194 -8.2E-05 0.000031 H -1.63712 2.148344 0.000025 H -2.91315 -7.5E-05 0.000007 H -1.63712 -2.14843 0.000026 H 0.83173 -2.15297 0.000015 H 0.831296 2.153325 0.000015
TS1
Atom X Y Z
O 2.214017 0.577364 0.099588 C 1.314469 -0.17405 -0.0044 C 0.631164 -1.31688 -0.1086 C -0.82099 -1.45256 -0.09815 C -1.62293 -0.39783 0.121901 C -1.01337 0.930792 0.394179 C -0.8321 1.867998 -0.57647 H 1.264937 -2.19225 -0.23142 H -1.21777 -2.44336 -0.30874 H -2.70417 -0.51577 0.062882 H -0.7199 1.060732 1.45749 H -0.2727 2.726898 -0.14766
IM1
Atom X Y Z
C -2.69504 -1.06365 0.000023 C -1.45592 -0.49671 0.000005 C -1.21718 0.927171 -1.3E-05 C -0.012 1.55016 -8E-06 C 1.309946 0.915773 -2.6E-05 C 1.666603 -0.35721 0.000014 O 2.181175 -1.41725 -2E-06 H 2.184674 1.567446 0.000122 H 0.024927 2.634988 0.00002 H -2.11216 1.546131 0.000015 H -0.51847 -1.09357 -4.6E-05 H -2.60688 -2.17021 -6.2E-05
154
TS2
Atom X Y Z
O -2.57008 -1.12974 -0.38629 C -1.92274 -0.26739 0.075935 C -1.20108 0.696538 0.591052 C -0.07246 1.306721 -0.17862 C 1.164687 0.764255 -0.32339 C 1.712415 -0.47237 0.186594 C 3.01894 -0.81446 -0.04974 H -1.46898 1.015444 1.598346 H -0.28552 2.270829 -0.63639 H 1.886744 1.342704 -0.90129 H 1.003208 -1.08388 0.767384 H 3.226599 -1.78691 0.451271
IM2
Atom X Y Z
C -3.49348 -0.33691 0.000058 C -2.1274 -0.41221 -2.9E-05 C -1.29131 0.769857 0.000018 C 0.064155 0.876105 -2.9E-05 C 0.978115 -0.27215 -0.00012 C 2.289585 -0.242 -8.5E-05 O 3.468378 -0.23052 0.000118 H 0.550586 -1.27266 0.000051 H 0.524536 1.859204 0.000015 H -1.85741 1.699945 0.000064 H -1.57189 -1.37048 -5.4E-05 H -3.91081 -1.3681 0.0001
TS3
Atom X Y Z
O -3.29409 -0.37229 -0.0029 C -2.11998 -0.28205 0.01177 C -0.81472 -0.19839 0.029164 C -0.0108 1.019433 -0.12656 C 1.32732 1.005526 0.008821 C 2.152774 -0.17547 0.395579 C 2.763436 -0.98587 -0.50134 H -0.25556 -1.12905 0.136625 H -0.5351 1.933887 -0.39336 H 1.840423 1.952427 -0.17517 H 2.2137 -0.28983 1.499858 H 3.301041 -1.78813 0.050618
155
IM3
Atom X Y Z
C 1.682158 1.543474 0.000042 C 2.224029 0.30226 -8.7E-05 C 1.569396 -0.98344 0.000039 C 0.217389 -1.26067 0.000149 C -0.86755 -0.39461 -0.00014 C -2.04121 0.040756 -4.9E-05 O -3.1468 0.541927 0.000027 H 0.609745 1.691002 0.000315 H -0.01388 -2.33425 -5.4E-05 H 2.234199 -1.84509 -3.1E-05 H 3.31529 0.245989 -0.00019 H 2.323735 2.420319 0.000012
TS4
Atom X Y Z
C -1.37808 1.561554 0.405081 C -1.97378 0.471265 -0.16333 C -1.3824 -0.85468 -0.34203 C -0.18582 -1.40004 -0.01168 C 0.950712 -0.72218 0.670809 C 1.730162 0.121051 0.043866 O 2.444327 0.859081 -0.51833 H 1.097811 -0.79029 1.747142 H -0.03 -2.45247 -0.24907 H -2.05658 -1.56765 -0.82864 H -3.01292 0.483864 -0.55287 H -2.11767 2.392045 0.413829
TS5
Atom X Y Z
C -1.07301 1.421784 0.024071 C -2.07046 0.527979 -0.12553 C -1.68646 -0.87995 -0.16209 C -0.38757 -1.18579 0.0646 C 0.555917 -0.11103 0.398061 C 1.944314 -0.25552 0.131265 O 2.842175 0.391192 -0.34904 H 0.448249 0.360945 1.375955 H -0.0174 -2.19807 -0.04533 H -2.41235 -1.65773 -0.39336 H -3.13807 0.771207 -0.24628 H -1.31418 2.489264 0.119104
156
P1
Atom X Y Z
C 1.594189 0.046369 -0.87705 C 1.138544 1.157282 -0.13251 C 0.444393 0.67032 1.000234 C 0.472964 -0.7454 0.953619 C 1.184767 -1.12829 -0.20763 C -1.84869 -0.0006 -0.69031 O -2.84123 0.000191 -0.12506 H -0.02261 1.273995 1.771338 H 0.031855 -1.41682 1.682842 H 1.372625 -2.14639 -0.53238 H 2.146477 0.088274 -1.81009 H 1.284529 2.201325 -0.38929
TS6
Atom X Y Z
C 1.275008 -1.14587 0.459232 C 1.659987 0.054496 -0.05941 C 0.908248 1.279538 -0.14001 C -0.44123 1.494146 0.039336 C -1.52074 0.573955 0.277015 C -1.46285 -0.72722 -0.17634 O -0.66643 -1.62714 -0.26118 H -2.5081 0.991638 0.443968 H -0.76507 2.529755 -0.09197 H 1.484881 2.15854 -0.43168 H 2.690282 0.1655 -0.44293 H 1.918866 -2.00265 0.213083
TS7
Atom X Y Z
O -1.34593 -0.40941 0.90176 C -0.91404 -0.8376 -0.2778 C 0.463355 -1.34641 -0.38407 C 1.479862 -0.54447 0.131645 C 1.262196 0.848969 0.233358 C 0.040263 1.434174 -0.15562 C -1.08033 0.657454 -0.51508 H 0.685985 -2.18627 -1.03856 H 2.492244 -0.92607 0.298342 H 2.079183 1.494436 0.547165 H -0.01994 2.514233 -0.28423 H -1.97783 1.106191 -0.93144
157
IM4
Atom X Y Z
C 1.232104 -0.9242 -0.23717 C 0.091179 -1.68274 -0.25795 O -0.99981 -0.97617 0.553123 C -1.47536 0.090693 -0.1192 C -0.82056 1.27204 -0.23887 C 0.556873 1.460103 0.145994 C 1.470474 0.445931 0.164693 H 2.105058 -1.44158 -0.64321 H 2.507445 0.721324 0.369702 H 0.900065 2.476803 0.334056 H -1.35835 2.101612 -0.69635 H -2.484 -0.0197 -0.53417
IM6
Atom X Y Z
C -1.44107 -0.701 0.190013 C -0.40657 -1.54905 -0.2913 C 0.873114 -1.27161 -0.25096 C 1.034256 1.069165 -0.0516 C -0.2613 1.454317 -0.23589 C -1.42947 0.677043 0.078156 O 1.420466 -0.07222 0.563798 H 1.716322 -1.70515 -0.7754 H 1.849112 1.701954 -0.41938 H -0.40079 2.44801 -0.66267 H -2.3725 1.218654 0.176156 H -2.36965 -1.15896 0.540346
TS10
Atom X Y Z
O 1.374762 -0.03244 0.770744 C -0.29343 -1.53808 -0.31896 C 0.951511 -0.87806 -0.33049 C 0.954948 0.857322 -0.21952 C -0.35562 1.407551 -0.19215 C -1.44011 0.619297 0.147482 C -1.37458 -0.81138 0.15483 H 1.825015 -1.26234 -0.85638 H 1.770034 1.400022 -0.70136 H -0.49608 2.415574 -0.57778 H -2.42627 1.08566 0.190796 H -2.32713 -1.31936 0.331628
158
IM7
Atom X Y Z
C 0.945491 0.76993 -0.28419 C 0.944067 -0.79757 -0.34782 C -0.3067 -1.54705 -0.28178 C -1.3897 -0.81303 0.141334 C -1.44183 0.633812 0.141216 C -0.35817 1.402086 -0.17686 O 1.415109 -0.02926 0.799125 H -0.45636 2.456217 -0.42361 H -2.41974 1.113651 0.222896 H -2.35234 -1.30961 0.298184 H 1.799334 -1.23679 -0.86489 H 1.749273 1.321539 -0.77702
TS11
Atom X Y Z
C -0.84727 1.252495 -0.04578 C 0.432155 1.058663 -0.49635 C 1.228487 -0.34236 -0.32162 C 0.06271 -1.25927 -0.54259 C -1.13738 -1.1304 0.113437 C -1.67139 0.160562 0.297683 O 1.778053 -0.05416 0.848801 H -1.20635 2.269962 0.096895 H -2.7291 0.300333 0.511471 H -1.80419 -1.9888 0.203662 H 1.96017 -0.45927 -1.14629 H 1.151165 1.872829 -0.48483
IM8
Atom X Y Z
C -1.74498 -0.88349 0.000039 C -1.97245 0.532717 0.000051 C -0.73512 1.16628 -0.00007 C 1.683353 0.435869 0.000035 C 0.28803 0.158203 -6.2E-05 C -0.37338 -1.11189 -5.6E-05 O 2.637901 -0.35708 0.000041 H -2.94234 1.018002 0.000141 H -2.51825 -1.64473 0.000086 H 0.128329 -2.07056 -0.00016 H 1.911776 1.531905 0.000041 H -0.55547 2.235825 -6.8E-05
159
TS13
Atom X Y Z
C -0.33575 1.119144 0.098748 C -1.68201 0.920387 -0.02861 C -1.95051 -0.50803 -0.12209 C -0.76442 -1.17892 -0.02582 C 0.31736 -0.19426 0.12508 C 1.759875 -0.56169 0.049653 O 2.601652 0.32452 -0.20345 H -2.93519 -0.95155 -0.22245 H -2.44831 1.691389 -0.03104 H 0.194573 2.05726 0.181396 H 0.9051 -0.72512 1.157159 H -0.59663 -2.24793 -0.03921
TS12
Atom X Y Z
C -0.45815 0.994669 0.583741 C -1.50135 0.660658 -0.42478 O -1.35576 -0.6375 -0.51806 C -0.31686 -0.97909 0.544528 C 0.998775 -1.15355 0.063092 C 1.57255 0.068466 -0.35379 C 0.859069 1.208528 -0.02492 H -0.75409 1.772148 1.30645 H 1.302629 2.198613 -0.08693 H 2.564318 0.127021 -0.80012 H 1.586261 -2.05474 0.219862 H -0.77725 -1.74115 1.178071
IM5
Atom X Y Z
C -2.455714 -0.9735 -0.11956 C -1.73104 -0.00458 -0.01104 C -1.00696 1.197287 0.112774 C 0.349314 1.453207 0.022569 C 1.535443 0.695541 -0.12476 C 1.777467 -0.6986 -0.05351 O 1.006787 -1.6433 0.178146 H -3.08807 -1.81896 -0.21479 H 2.864086 -0.93679 -0.21811 H 2.441038 1.285113 -0.26066 H 0.555855 2.525596 0.06731 H -1.63828 2.075359 0.24223
160
TS8
Atom X Y Z
O -0.93331 -1.48953 0.395571 C 1.651907 -0.59444 -0.08602 C 1.386956 0.785563 -0.24476 C 0.198868 1.49878 0.041722 C -1.1132 1.115652 0.219013 C -1.67564 -0.17693 -0.03816 C -1.79894 -1.42824 -0.32687 H 2.688773 -0.87222 -0.412 H 2.249263 1.3833 -0.53501 H 0.341364 2.579331 0.124796 H -1.8286 1.893118 0.466455 H -2.81703 -0.26967 -0.19835
TS9
Atom X Y Z
C -1.54764 -0.50508 0.198279 C -1.33169 0.85199 0.07201 C -0.07403 1.471895 -0.24052 C 1.177906 0.93935 -0.05576 O 1.46869 -0.20003 0.555473 C 0.661342 -1.45864 -0.26557 C -0.62461 -1.48443 -0.252 H 1.469809 -1.96143 -0.76948 H 2.036402 1.503449 -0.45155 H -0.09507 2.476151 -0.66471 H -2.19378 1.51703 0.165419 H -2.53454 -0.82549 0.537841
Cyclopentadienyl anion
Atom X Y Z
C 1.202957 0.049914 -2.6E-05 C 0.32422 1.159454 -0.00015 C -1.00255 0.666643 -7.2E-05 C -0.94384 -0.74744 0.000168 C 0.419204 -1.12858 0.000075 H 0.61665 2.20513 -0.00014 H 2.287813 0.095008 0.000716 H 0.797289 -2.14641 -0.00063 H -1.79502 -1.42156 -0.00051 H -1.90668 1.267894 0.000606
CO
Atom X Y Z
C 0 0 -0.64439 O 0 0 0.483295
161
C6H5
.-
Atom X Y Z
C -1.16261 -0.45078 0.000007 C 0.000001 -1.23131 0.000243 C -1.16261 -0.45079 -0.00018 C -0.70606 0.901241 0.000068 C 0.706059 0.901241 -0.00022 H 2.191222 -0.78956 -0.00011 H 1.343803 1.780757 0.000232 H -1.34381 1.780755 0.000759 H -2.19122 -0.78956 -0.00038
CHO.
Atom X Y Z
C 0.06177 0.58372 0 O 0.06177 -0.59059 0 H -0.86478 1.222377 0